How can a reboot make a program running as expected (or not...) ?
in short - it cant. The compiler is going to produce the same .HEX file no matter what.

If you had a problem with your PC that caused the compiler to generate a bad .HEX file at compile time, I suspect you would be having a great deal more problems than just compiling a PBP program.

My guess would be you had something loaded in memory, from an old file, that wasn't being updated by your programmer at program time.

Re-booting or not re-booting your PC should have zero affect on the compiled .HEX file that PBP produced at compile time.

For example, you compile a program, then you re-boot your PC. How would re-booting your PC alter your previously compiled .HEX file? If it does - you have major issues with your PC..;o)

If your device programmer is not reloading the new version .HEX file into memory after each compile, prior to progamming the device, that would be an issue.