I moved from 2016 to 2023 (new employment) and the best fit alignment is not working as I would expected. For example I get an "Error in A1" trying my normal 6 dof (YZ, YZ, XZ) using 3 edge points on a common plane. If I use the 3 same three poin

Try changing measure order to both. It worked just fine for me.

PART NAME  : delete
REV NUMBER : 
SER NUMBER : 
STATS COUNT : 1
GD&T STANDARD : ASME Y14.5 - 2009/2018
 
STARTUP    =ALIGNMENT/START,RECALL:USE_PART_SETUP,LIST=YES
            ALIGNMENT/END
            MODE/MANUAL
            FORMAT/TEXT,OPTIONS, , , , ;NOM,MEAS,TOL,DEV,OUTTOL, , 
            LOADPROBE/4WAY_30X2_STAR
            TIP/T1A0B0, SHANKIJK=0, 0, 1, ANGLE=0
PNT1       =FEAT/CONTACT/EDGE POINT/DEFAULT,CARTESIAN
            THEO/<4.625,2.7747,0.95>,<0,0,1>,<1,0,0>
            ACTL/<12.4839,1.0726,0.95>,<0,0,1>,<1,0,0>
            TARG/<4.625,2.7747,0.95>,<0,0,1>,<1,0,0>
            MEASURE ORDER=BOTH
            SHOW FEATURE PARAMETERS=YES
              VOID DETECTION=NO
              SURFACE1=THICKNESS_NONE,0
              SURFACE2=THICKNESS_NONE,0
              MEASURE MODE=NOMINALS
              RMEAS=NONE,NONE,NONE
              AUTO WRIST=NO
              GRAPHICAL ANALYSIS=NO
              FEATURE LOCATOR=NO,NO,""
            SHOW CONTACT PARAMETERS=YES
              DEPTH=0
              SAMPLE HITS=1,SPACER=0,INDENT1=0
              AVOIDANCE MOVE=BOTH,DISTANCE BEFORE=0.3937,DISTANCE AFTER=0.3937,DIRECTION=ALONG FEATURE VECTOR
              ONERROR=NO
PNT2       =FEAT/CONTACT/EDGE POINT/DEFAULT,CARTESIAN
            THEO/<-2.1729,1.375,0.95>,<0,0,1>,<0,-1,0>
            ACTL/<5.7464,-0.2665,0.95>,<0,0,1>,<0,-1,0>
            TARG/<-2.1729,1.375,0.95>,<0,0,1>,<0,-1,0>
            MEASURE ORDER=BOTH
            SHOW FEATURE PARAMETERS=YES
              VOID DETECTION=NO
              SURFACE1=THICKNESS_NONE,0
              SURFACE2=THICKNESS_NONE,0
              MEASURE MODE=NOMINALS
              RMEAS=NONE,NONE,NONE
              AUTO WRIST=NO
              GRAPHICAL ANALYSIS=NO
              FEATURE LOCATOR=NO,NO,""
            SHOW CONTACT PARAMETERS=YES
              DEPTH=0
              SAMPLE HITS=1,SPACER=0,INDENT1=0
              AVOIDANCE MOVE=BOTH,DISTANCE BEFORE=0.3937,DISTANCE AFTER=0.3937,DIRECTION=ALONG FEATURE VECTOR
              ONERROR=NO
PNT3       =FEAT/CONTACT/EDGE POINT/DEFAULT,CARTESIAN
            THEO/<2.3332,1.375,0.95>,<0,0,1>,<0,-1,0>
            ACTL/<10.338,-0.2673,0.95>,<0,0,1>,<0,-1,0>
            TARG/<2.3332,1.375,0.95>,<0,0,1>,<0,-1,0>
            MEASURE ORDER=BOTH
            SHOW FEATURE PARAMETERS=YES
              VOID DETECTION=NO
              SURFACE1=THICKNESS_NONE,0
              SURFACE2=THICKNESS_NONE,0
              MEASURE MODE=NOMINALS
              RMEAS=NONE,NONE,NONE
              AUTO WRIST=NO
              GRAPHICAL ANALYSIS=NO
              FEATURE LOCATOR=NO,NO,""
            SHOW CONTACT PARAMETERS=YES
              DEPTH=0
              SAMPLE HITS=1,SPACER=0,INDENT1=0
              AVOIDANCE MOVE=BOTH,DISTANCE BEFORE=0.3937,DISTANCE AFTER=0.3937,DIRECTION=ALONG FEATURE VECTOR
              ONERROR=NO
ALIGN_1    =ALIGNMENT/START,RECALL:STARTUP,LIST=YES
              ALIGNMENT/BF3D,LEAST_SQR,CREATE WEIGHTS=NO,ROTANDTRANS,USE SCALING=NO,7.8585,-1.6419,0,-0.0094,0,0
              ITERATEANDREPIERCECAD=NO
              Deviation Threshold=0.01
              SHOWALLINPUTS=YES,SHOWALLPARAMS=YES
                ID=PNT1,Points,,1,YES,YES,NO,YES
                ID=PNT2,Points,,1,YES,NO,YES,YES
                ID=PNT3,Points,,1,YES,NO,YES,YES
                ID=
            ALIGNMENT/END
DIM 1= LOCATION OF POINT PNT1  UNITS=IN ,$
GRAPH=OFF  TEXT=OFF  MULT=10.00  OUTPUT=BOTH  HALF ANGLE=NO
X       4.6250     4.6250     0.0000     0.0000     0.0000     0.0000
Z       0.9500     0.9500     0.0000     0.0000     0.0000     0.0000
T       0.0000     0.0000     0.0000     0.0000     0.0000     0.0000
END OF DIMENSION 1
DIM 2= LOCATION OF POINT PNT2  UNITS=IN ,$
GRAPH=OFF  TEXT=OFF  MULT=10.00  OUTPUT=BOTH  HALF ANGLE=NO
Y       1.3750     1.3750     0.0000     0.0000     0.0000     0.0000
Z       0.9500     0.9500     0.0000     0.0000     0.0000     0.0000
T       0.0000     0.0000     0.0000     0.0000     0.0000     0.0000
END OF DIMENSION 2
DIM 3= LOCATION OF POINT PNT3  UNITS=IN ,$
GRAPH=OFF  TEXT=OFF  MULT=10.00  OUTPUT=BOTH  HALF ANGLE=NO
Y       1.3750     1.3750     0.0000     0.0000     0.0000     0.0000
Z       0.9500     0.9500     0.0000     0.0000     0.0000     0.0000
T       0.0000     0.0000     0.0000     0.0000     0.0000     0.0000
END OF DIMENSION 3

I will in the morning but I think its something global as I have this issue with the last couple of programs I have had my hands on since I started.  I am having this issue on all of them as I am rewriting programs due to a fixturing system they have here. Plus I am using flow control to bypass the manual.  It had always gotten me real close and I have been doing this way for over 10 years. Not all my parts are square to the world so I use this instead of offsetting features to create the 321 features needed for that route.

I will in the morning but I think its something global as I have this issue with the last couple of programs I have had my hands on since I started.  I am having this issue on all of them as I am rewriting programs due to a fixturing system they have here. Plus I am using flow control to bypass the manual.  It had always gotten me real close and I have been doing this way for over 10 years. Not all my parts are square to the world so I use this instead of offsetting features to create the 321 features needed for that route.