FYI, just started playing around with Shadow, and it seems that if you're mind flaying when Spirit Tap expires, you lose a tick of flay. Just reproduced it 5 times in a row doing that, anyway.
edit: Actually on playing further, yeah, just seems like it randomly only does 2 ticks for no good reason. Tried seeing if it was just the combat log messing up, but it seems that it is indeed only ticking twice and not just faking it. Also tried just flay alone with no other effects running to test out the "effect expiring interrupting it" theory, but no dice.