I have been playing Spriest for a while now and i have seen from every now and then when i mind flay its seems to not refresh the Shadow word pain if it is at 2 too 3 seconds. The shadow word pain will just dissapear just wondering if this is a bugg our not.
The only other thing I can think of is if you previous refreshed SW:P at a time that wasn't a multiple of 3 seconds, then perhaps SW:P is disappearing on the last tick of damage even if there is 1 or 2 sec left on the duration?
It has been like this ever since beta.
It happens when SWP wont tick again on the current duration, for example if it ticks at 2.5 seconds left on the debuff, it wont refresh after that for whatever reason.
DKs had the same bug with glyth of disease and plague strike last patch... this got fixed. Our talent doesn't get fixed >.>