PC-DMIS giving bad results

Workplane?
Do you have points made at your cylinder centroids? For at least your cylinder3 I would think you'd want points to evaluate(top/bottom), not a rotated cylinder's center axis.

Without seeing more code no one can really help you find mistake.. 1thing. LEVEL AND ROTATE ALWAYS. Then define X-Y-Z in any order... Your alignment is rotating to X, but then your distance is // to Y. That means if you use location you would have 1 number and your DISTANCE dimension would be different. DISTANCE is kinda like " location with possible different alignment " . I'm guessing your just comparing apples to oranges. If the numbers don't come out on CAD, you are kinda dead in the water before you start.

Try using the intersection of the cylinder and the part face to create a construction instead of a pierce point.

=alignment/start,recall:use_part_setup,list=yes
alignment/end
mode/manual
format/text,options,id,headings,symbols, ;nom,tol,meas,maxmin,dev,devang,outtol
movespeed/ 300
prehit/0.125
retract/0.125
touchspeed/ 3.5
loadprobe/tool_2
tip/t1a0b0, shankijk=0, 0, 1, angle=0
startpoint =feat/point,cartesian
theo/<0,0,0>,<0,0,1>
actl/<9.5192,14.6362,-23.982>,<0,0,1>
readpoint/
a1 =alignment/start,recall:startup,list=yes
alignment/trans,xaxis,startpoint
alignment/trans,yaxis,startpoint
alignment/trans,zaxis,startpoint
alignment/end
mode/dcc
move/increment,<0,0,0.3>
point2 =feat/contact/vector point/default,cartesian
theo/<-0.1926,-0.4883,0.03>,<0,0,1>
actl/<-0.1926,-0.4883,0.025>,<0,0,1>
targ/<-0.1926,-0.4883,0.03>,<0,0,1>
snap=no
show feature parameters=no
show contact parameters=yes
avoidance move=both,distance=0.15
show hits=no
point3 =feat/contact/vector point/default,cartesian
theo/<0.0375,-0.3488,0.03>,<0,0,1>
actl/<0.0375,-0.3489,0.0247>,<0,0,1>
targ/<0.0375,-0.3488,0.03>,<0,0,1>
snap=no
show feature parameters=no
show contact parameters=yes
avoidance move=both,distance=0.15
show hits=no
point4 =feat/contact/vector point/default,cartesian
theo/<-0.1964,0.34,0.03>,<0,0,1>
actl/<-0.1964,0.34,0.0252>,<0,0,1>
targ/<-0.1964,0.34,0.03>,<0,0,1>
snap=no
show feature parameters=no
show contact parameters=yes
avoidance move=both,distance=0.15
show hits=no
point5 =feat/contact/vector point/default,cartesian
theo/<0.0263,0.4712,0.03>,<0,0,1>
actl/<0.0263,0.4711,0.025>,<0,0,1>
targ/<0.0263,0.4712,0.03>,<0,0,1>
snap=no
show feature parameters=no
show contact parameters=yes
avoidance move=both,distance=0.15
show hits=no
plane1 =feat/plane,cartesian,triangle,no,least_sqr
theo/<-0.0813,-0.0065,0.03>,<0,0,1>
actl/<-0.0813,-0.0065,0.025>,<0.0013343,-0.0002879,0.9999991>
constr/plane,bf,point2,point5,point4,point3,,
outlier_removal/off,3
filter/off,wavelength=0
align2 =alignment/start,recall:a1,list=yes
alignment/level,zplus,plane1
alignment/trans,zaxis,plane1
alignment/end
prehit/0.045
retract/0.045
cylinder1 =feat/contact/cylinder/default,cartesian,in,least_sqr
theo/<0,0,-0.03>,<0,0,1>,0.194,0.06
actl/<0.0012,0.0174,-0.03>,<0.001373,0.001417,0.9999981>,0.1937,0.06
targ/<0,0,-0.03>,<0,0,1>
start ang=0,end ang=360
angle vec=<1,0,0>
direction=ccw
show feature parameters=no
show contact parameters=yes
numhits=6,numlevels=2,depth=0.03,end offset=0.01,pitch=0
sample method=sample_hits
sample hits=0,spacer=0
avoidance move=both,distance=0.15
find hole=disabled,onerror=no,read pos=no
show hits=no
align3 =alignment/start,recall:align2,list=yes
alignment/level,zplus,plane1
alignment/trans,zaxis,plane1
alignment/trans,xaxis,cylinder1
alignment/trans,yaxis,cylinder1
alignment/end
move/increment,<0,0,2>
move/increment,<2.35,0,0>
cylinder2 =feat/contact/cylinder/default,cartesian,in,least_sqr
theo/<2.25,0,0>,<0,0,1>,0.194,0.09
actl/<2.2495,-0.002,0>,<-0.0024484,-0.0005462,0.9999969>,0.1937,0.09
targ/<2.25,0,0>,<0,0,1>
start ang=0,end ang=360
angle vec=<1,0,0>
direction=ccw
show feature parameters=no
show contact parameters=yes
numhits=6,numlevels=2,depth=0.01,end offset=0.03,pitch=0
sample method=sample_hits
sample hits=0,spacer=0
avoidance move=both,distance=0.3
find hole=disabled,onerror=no,read pos=no
show hits=no
line1 =feat/line,cartesian,unbounded,no
theo/<2.25,0,-0.015>,<-1,0,0>
actl/<2.2495,-0.002,-0.015>,<-0.9999996,0.0008817,0>
constr/line,bf,2d,cylinder2,cylinder1,,
outlier_removal/off,3
filter/off,wavelength=0
align4 =alignment/start,recall:startup,list=yes
alignment/level,zplus,plane1
alignment/trans,zaxis,plane1
alignment/trans,xaxis,cylinder1
alignment/trans,yaxis,cylinder1
alignment/rotate,xminus,to,line1,about,zplus
alignment/end
move/increment,<0,0,2>
loadprobe/tool_15
tip/t1a0b0, shankijk=0, 0, 1, angle=0
move/increment,<0,-4,0>
move/increment,<1.3,0,0>
tip/t1a-35b-90, shankijk=-0.5736, 0, 0.8192, angle=-90
prehit/0.125
retract/0.125
point6 =feat/contact/vector point/default,cartesian
theo/<0.3883,0.5396,0.1367>,<-0.5735764,0,0.819152>
actl/<0.3905,0.5397,0.1336>,<-0.5735764,0,0.819152>
targ/<0.3883,0.5396,0.1367>,<-0.5735764,0,0.819152>
snap=no
show feature parameters=no
show contact parameters=yes
avoidance move=both,distance=0.5
show hits=no
point7 =feat/contact/vector point/default,cartesian
theo/<0.3168,0.473,0.0867>,<-0.5735764,0,0.819152>
actl/<0.3189,0.4728,0.0834>,<-0.5735764,0,0.819152>
targ/<0.3168,0.473,0.0867>,<-0.5735764,0,0.819152>
snap=no
show feature parameters=no
show contact parameters=yes
avoidance move=both,distance=0.15
show hits=no
point8 =feat/contact/vector point/default,cartesian
theo/<0.3186,-0.4312,0.088>,<-0.5735764,0,0.819152>
actl/<0.321,-0.4315,0.0844>,<-0.5735764,0,0.819152>
targ/<0.3186,-0.4312,0.088>,<-0.5735764,0,0.819152>
snap=no
show feature parameters=no
show contact parameters=yes
avoidance move=both,distance=0.15
show hits=no
point9 =feat/contact/vector point/default,cartesian
theo/<0.4365,-0.5322,0.1705>,<-0.5735764,0,0.819152>
actl/<0.4392,-0.5323,0.1673>,<-0.5735764,0,0.819152>
targ/<0.4365,-0.5322,0.1705>,<-0.5735764,0,0.819152>
snap=no
show feature parameters=no
show contact parameters=yes
avoidance move=both,distance=0.3
show hits=no
plane2 =feat/plane,cartesian,triangle,no,least_sqr
theo/<0.3651,0.0123,0.1205>,<-0.5735764,0,0.819152>
actl/<0.3674,0.0122,0.1172>,<-0.5743277,-0.0003714,0.8186254>
constr/plane,bf,point6,point9,point8,point7,,
outlier_removal/off,3
filter/off,wavelength=0
cylinder3 =feat/contact/cylinder/default,cartesian,in,least_sqr
theo/<0.7281,0,0.2805>,<-0.5735764,0,0.819152>,0.6287,0.7151
actl/<0.7335,-0.0094,0.2843>,<-0.574195,-0.0000904,0.8187185>,0.6293,0.7151
targ/<0.7281,0,0.2805>,<-0.5735764,0,0.819152>
start ang=0,end ang=360
angle vec=<0.819152,0,0.5735764>
direction=ccw
show feature parameters=no
show contact parameters=yes
numhits=8,numlevels=2,depth=0.1,end offset=0.515,pitch=0
sample method=sample_hits
sample hits=0,spacer=0
avoidance move=both,distance=0.5
find hole=disabled,onerror=no,read pos=no
show hits=no
move/increment,<0,0,4.5>
move/increment,<0,-2.5,0>
tip/t1a-95b0, shankijk=0, -0.9962, -0.0872, angle=0
move/increment,<0,-2.5,0>
move/increment,<0,-2,0>
move/increment,<0,0,-9.5>
point10 =feat/contact/vector point/default,cartesian
theo/<0.0212,-0.6137,-0.125>,<0,0,-1>
actl/<0.0212,-0.6136,-0.0961>,<0,0,-1>
targ/<0.0212,-0.6137,-0.125>,<0,0,-1>
snap=no
show feature parameters=no
show contact parameters=yes
avoidance move=both,distance=0.225
show hits=no
point11 =feat/contact/vector point/default,cartesian
theo/<0.3233,-0.2962,-0.125>,<0,0,-1>
actl/<0.3232,-0.2962,-0.0958>,<0,0,-1>
targ/<0.3233,-0.2962,-0.125>,<0,0,-1>
snap=no
show feature parameters=no
show contact parameters=yes
avoidance move=both,distance=0.15
show hits=no
point12 =feat/contact/vector point/default,cartesian
theo/<0.6381,-0.5274,-0.125>,<0,0,-1>
actl/<0.638,-0.5274,-0.0956>,<0,0,-1>
targ/<0.6381,-0.5274,-0.125>,<0,0,-1>
snap=no
show feature parameters=no
show contact parameters=yes
avoidance move=both,distance=0.15
show hits=no
point13 =feat/contact/vector point/default,cartesian
theo/<1.1921,-0.4793,-0.125>,<0,0,-1>
actl/<1.192,-0.4791,-0.0947>,<0,0,-1>
targ/<1.1921,-0.4793,-0.125>,<0,0,-1>
snap=no
show feature parameters=no
show contact parameters=yes
avoidance move=both,distance=0.15
show hits=no
point14 =feat/contact/vector point/default,cartesian
theo/<1.7334,-0.3241,-0.125>,<0,0,-1>
actl/<1.7333,-0.3241,-0.0938>,<0,0,-1>
targ/<1.7334,-0.3241,-0.125>,<0,0,-1>
snap=no
show feature parameters=no
show contact parameters=yes
avoidance move=both,distance=0.15
show hits=no
point15 =feat/contact/vector point/default,cartesian
theo/<2.0356,-0.5301,-0.125>,<0,0,-1>
actl/<2.0355,-0.5301,-0.0932>,<0,0,-1>
targ/<2.0356,-0.5301,-0.125>,<0,0,-1>
snap=no
show feature parameters=no
show contact parameters=yes
avoidance move=both,distance=0.3
show hits=no
plane3 =feat/plane,cartesian,triangle,no,least_sqr
theo/<0.9906,-0.4618,-0.125>,<0,0,-1>
actl/<0.9905,-0.4617,-0.0949>,<0.0014699,-0.0002264,-0.9999989>
constr/plane,bf,point10,point15,point14,point13,point12,point11,,
outlier_removal/off,3
filter/off,wavelength=0
move/increment,<0,-2.85,0>
move/increment,<0,0,10>
align5 =alignment/start,recall:startup,list=yes
alignment/level,zminus,plane3
alignment/trans,zaxis,plane3
alignment/trans,xaxis,cylinder1
alignment/trans,yaxis,cylinder1
alignment/rotate,xminus,to,line1,about,zminus
alignment/end
dim loc1= location of cylinder cylinder3 units=in ,$
graph=off text=off mult=10.00 output=both half angle=no
ax nominal +tol -tol meas max min dev outtol
y 0.0000 0.0010 0.0010 -0.0095 0.3052 -0.3241 -0.0095 0.0085 <--------
end of dimension loc1
point1 =feat/point,cartesian,no
theo/<1.012,0,0>,<-0.5735764,0,0.819152>
actl/<0.9994,-0.0094,0>,<-0.572991,-0.0002757,0.8195616>
constr/point,pierce,cylinder3,plane3
point16 =feat/point,cartesian,no
theo/<0.6838,0,0.4687>,<-0.5735764,0,0.819152>
actl/<0.6919,-0.0095,0.4399>,<-0.572991,-0.0002757,0.8195616>
constr/point,pierce,cylinder3,plane2
dim dist1= 2d distance from point point16 to cylinder cylinder1 par to xaxis,no_radius units=in,$
graph=off text=off mult=10.00 output=both
ax nominal +tol -tol meas max min dev outtol
m 0.6830 0.0050 0.0050 0.6919 0.6919 0.6919 0.0089 0.0039 -------->
dim dist2= 2d distance from point point1 to cylinder cylinder1 par to xaxis,no_radius units=in,$
graph=off text=off mult=10.00 output=both
ax nominal +tol -tol meas max min dev outtol
m 1.0120 0.0050 0.0050 0.9994 0.9994 0.9994 -0.0126 0.0076 <--------

Thanks but I have tried this as well and the results are the same. I uploaded the whole program in the comment above.

So when you run this OFFLINE, your nominals are correct ?

LAST TIME ..... LEVEL AND ROTATE. Then define X-Y-Z in any order. No exceptions, Take this to heart.

Make sure both of your probes and all their respective angles are calibrated properly. look up and implement a "Master Probe" if you haven't already.

Yes when I run it offline my nominals are correct. I used Auto-align to my Datums called out. And I tried level and rotate and I get the same readings.

I am checking the distance to Y the drawing is an error. And for the dimensions to the pierce points I am checking on X

I had made a pervious program with a single probe, calibrated all angles and the results were the same.