+1 on this, it's pretty annoying.
In mi case (5.40, Win7), I lose use of the shortcuts whenever I have focus on a FX window. But then,
SPACE BAR for PLAY/STOP does work. Or my shortcuts for cycling among my inserts and the one for closing them, probably having something to do with the FX window being focused. Then why not all the rest?
EDIT - This seems to be the thread to go:
http://forum.cockos.com/showthread.p...ight=shortcuts