Hi all. I have had exactly the same problem — I’m on Premiere Pro 8.1 and the bug is still there.
Symptoms: you apply a mask to an effect (any effect, any mask) and immediately the image is offset vertically and horizontally by a long way. It often gets cropped in the process, and there is no way to bring it back into the right position.
Solution: nest the clip in a sequence WITH THE SAME DIMENSIONS AS THE CLIP. Then you can apply the mask in that sequence, and bring it in to the one you were working on. Clumsy, but it works. The bug seems to be caused by a sequence with different dimensions from the clip you’re working on (something that is often the case with SFX composites).
Hope this helps.