Heheheh, I should have explained things better. Can tell I was half-asleep when I posted the above.
Actually you have something there. It works fine now. The executables were created and sitting inside the 'projects' directory where the samples were. So I assumed they should see them, but of course the executable is looking for the samples in a folder called 'projects'. So moving the executables one directory up, outside of the 'projects' directory, and it all worked fine.

I'm guessing it's to do with how the paths are saved with the info that is attached to the executable stub. ie. not so much as a bug or glitch, as a gotcha (user issue

).