Thanks for the reply! It's relieving to hear that I'm not the only one this has happened to. :O
I rendered that specific masked part, and the problem was still there, unfortunately. I'm not quite sure if I do understand your suggestion completely...correct me if I'm wrong, you're saying just to move the said keyframe a frame over...so...that makes it where the mask isn't lined up correctly in the pan/crop window, but it should look right in the preview, or when I render it again? I tried moving some keyframes, trying to get the masks to line up right, rendered it multiple times, and I still just can't seem to get it to work. -_- It just boggles my mind that the masking looks correct in the pan/crop window, but when I render it, it's way off. Let me know if I'm way off base from what you're trying to explain to me.
I also did double check to make sure the FPS of the anime matched my problem settings, and they are correct.
I also noticed that frames that the masks are off are all keyframes...the rest of the frames are lined up perfectly in the preview, but the keyframes or not...which doesn't makes sense to me, at all.