Trying to measure a 3mm hole with a 1mm probe

After some more experimenting, the 5mm probe I use to do the initial alignment finds the hole exactly when I use the "move to" button. The second 1mm probe is off in both x and y. I am going to try to do another alignment after using the 1mm probe and see if that fixes it. Is that normal behavior for PC DMIS?

That sounds more like a probe calibration problem - the relationship between the two different probes is incorrect.  Search this forum, there are many, many, many posts on the topic of probe calibration.

Both probes were calibrated before I started measuring. I just calibrated them again for good measure. I also manually took some hits with the 1mm probe. It is now off by -1.127" in x, .025" in z and .924" in y. It looks like the probe thinks that the part is somewhere completely different than where it is. I think there must be something that I have to do with alignments when changing probe tips. I use a probe rack and the machine does it automatically. I think that there is something very basic that I am missing that is so basic that nobody here would even think to respond with the answer. Here is the code for my program so far. 

PART NAME : measurement test 1
REV NUMBER :
SER NUMBER :
STATS COUNT : 1

STARTUP =ALIGNMENT/START,RECALL:USE_PART_SETUP,LIST=YES
ALIGNMENT/END
MODE/MANUAL
FORMAT/TEXT,OPTIONS, ,HEADINGS,SYMBOLS, ;NOM,TOL,MEAS,DEV,OUTTOL, ,
LOADPROBE/5MM50L PROBE
TIP/T1A0B0, SHANKIJK=0, 0, 1, ANGLE=0
MAN_ALIGN =GROUP/SHOWALLPARAMS=NO
ENDGROUP/ID=MAN_ALIGN
DCC_ALIGN =GROUP/SHOWALLPARAMS=NO
ENDGROUP/ID=DCC_ALIGN
SCN1 =FEAT/SCAN,LINEAROPEN,NUMBER OF HITS=397,SHOW HITS=YES,SHOWALLPARAMS=NO
MEAS/SCAN
BASICSCAN/LINE,NUMBER OF HITS=397,SHOW HITS=YES,SHOWALLPARAMS=NO
*A BUNCH OF HITS*
ENDSCAN
ENDMEAS/
MOVE/POINT,NORMAL,<1.8409,-1.1827,1.4011>
LOADPROBE/1MM PROBE WITH EXTENSIONS
TIP/T1A0B0, SHANKIJK=0.0001, 0, 1, ANGLE=0.0959
MODE/MANUAL
PLN4 =FEAT/PLANE,CARTESIAN,TRIANGLE
THEO/<1.063,-3.6554,-0.1457>,<-1,0,0>
ACTL/<-0.0641,-2.8459,-0.1078>,<-0.9999983,-0.0001729,0.0018597>
MEAS/PLANE,3
HIT/BASIC,NORMAL,<1.063,-2.2793,-0.175>,<-1,0,0>,<-0.0644,-1.4773,-0.1108>,USE THEO=YES
HIT/BASIC,NORMAL,<1.063,-3.5447,-0.0538>,<-1,0,0>,<-0.064,-2.8064,-0.0567>,USE THEO=YES
HIT/BASIC,NORMAL,<1.063,-5.1423,-0.2083>,<-1,0,0>,<-0.064,-4.2542,-0.1558>,USE THEO=YES
ENDMEAS/
PLN5 =FEAT/PLANE,CARTESIAN,TRIANGLE
THEO/<1.7903,-2.646,-0.0098>,<0,0,1>
ACTL/<0.5752,-1.938,0.0156>,<0.0000849,-0.0000348,1>
MEAS/PLANE,3
HIT/BASIC,NORMAL,<1.4314,-4.7782,-0.0098>,<0,0,1>,<0.2498,-3.7312,0.0155>,USE THEO=YES
HIT/BASIC,NORMAL,<1.5476,-1.8087,-0.0098>,<0,0,1>,<0.2462,-1.5491,0.0156>,USE THEO=YES
HIT/BASIC,NORMAL,<2.3918,-1.3511,-0.0098>,<0,0,1>,<1.2295,-0.5336,0.0156>,USE THEO=YES
ENDMEAS/
PLN6 =FEAT/PLANE,CARTESIAN,TRIANGLE
THEO/<2.8752,-0.9843,-0.1258>,<0,1,0>
ACTL/<1.6836,-0.0602,-0.0896>,<-0.0005733,0.9999913,-0.0041359>
MEAS/PLANE,3
HIT/BASIC,NORMAL,<1.9252,-0.9843,-0.0888>,<0,1,0>,<0.7465,-0.0607,-0.0615>,USE THEO=YES
HIT/BASIC,NORMAL,<2.9035,-0.9843,-0.1953>,<0,1,0>,<1.608,-0.0605,-0.146>,USE THEO=YES
HIT/BASIC,NORMAL,<3.7969,-0.9843,-0.0934>,<0,1,0>,<2.6961,-0.0595,-0.0615>,USE THEO=YES
ENDMEAS/

Is it possible for you to edit this post and cut your program text, and paste it into an Insert > Code block so it's more readable?

I tried, but do you know which language I was supposed to select to actually format the text? PC DMIS is not an option for type of code.

It looks like an alignment that is done using one probe is not carried over to other probes. I assume that this is normal and expected behavior and I should be creating new alignments for each probe that I load? Will I also need to create new alignments when I change the angle of the probe head but keep the same probe?

It looks like an alignment that is done using one probe is not carried over to other probes. I assume that this is normal and expected behavior and I should be creating new alignments for each probe that I load? Will I also need to create new alignments when I change the angle of the probe head but keep the same probe?