Strange problem for sure. I would create two copies of the same program. Something simple
like blink1.bas and blink2.bas. Compile blink1.bas and keep it in a separate directory outside
of my usual code files directory.

Compile blink2.bas and compare the two .hex files. The next time this happens, recompile
blink2.bas and compare the .hex files again.

If they're different you have it narrowed down to some part of the compile process. That
should make it easier to nail down.

I would also try reinstalling stuff one at a time. I.E. reinstall MCS, then test it before you
reinstall PBP or MPLAB. It may be only one of these getting screwed up.

I had some odd problems recently after installing XP service pack 3 where XP would not allow
me to save a ton of various file extensions. I had to do this;
http://www.winhelponline.com/blog/re...in-windows-xp/