I have a home made 3 axis CNC router with a spring loaded pin that sets off a proximity switch to set the tool to the top of the table.  I've written a program to move the tool to a fixed position when I push the button "Auto Tool Zero".  This worked fine until I upgraded from R3.042.040 to R3.043.066.  Now what happens is after I home the machine (X & Y axis) and go to set the tool (Z axis) the tool moves correctly to the X & Y machined coordinates like it's suppose to, moves down, sets off the proximity switch and stops.  It's suppose to set off the proximity switch and go up to 2" in Z.  If I reset Mach3 and move the tool off of the proximity switch pin and then hit "Auto Tool Zero", it works correctly.  Shown below are the two Programs that I use for homing the machine and using the "Auto Tool Zero" button.

To Home the Machine:
DoButton(23)
Refcombination(9)

To set the tool:
Call SetDRO(2,2.)
Code "G0 G53 X33.619 Y.181"
Code "G28.1 Z1.9"
While IsMoving()
Wend
Code "G53 G0 Z2.0"
While IsMoving()
Wend
Call SetDRO(2,2.)

If anyone has any suggestions how to fix this problem, I would sure appreciate it.

066 has faults as you have discovered, go back to an earlier rev like I have done. You can get previous versions from the ftp site.
ftp://machsupport.com/Mach/
Hood