I have tried using another program now (DVD Shrink & VobEdit instead of DVD Decrypter). Again, premiere does something to it that isn't visible in the source file. Again, it happens at the exact same time. My brain hurts.
I checked if it happens simultaneusly with the layer change. It doesn't, but it's right after. The layer change happens as Obi-Wan appear behind Jango's Slave I before the asteroid field and the blockiness begins the second C-3PO becomes visible in a big establishing shot. This could be all his fault. Though I'm leaning more and more towards MBJ's suggestion, that "there might be a flag in the MPEG that is messing with Premiere."
This does seem the most logical problem, but I don't understand it at all. More importantely, I have no idea how to fix it or if it is even "fixable".
A side note/question: What is the most common used program for fan edits? Because in the worst case scenario, I might have to do this all over.