Kevin,
I havent used Mach 3 software but I suppose if it was not correctly setup it could have give problems with drive controllers but I think it would be more with stability issues rather than damaging boards.
What is wrong with the supplied software for controlling the machine? If it is purley for handling different file types then a decent post processor could be what you need. What code type does the machine run, ie Gcode or ESSI?
If you design your drawings in say Autocad then the post processor should convert the file to the correct code type you need.
There are many cnc code converters out there, some free and some not. Searching for cnc code converter on google should find you something useful.

regards

Ian