I've tried really hard to replicate this as to what exactly happens and when, but with no luck. All that I know is that in both 2.5 and classic mode, when you try to switch a tile inbetween 8 bit and 4 bit, weird things happen. Sometimes the two leftmost tile columns on the tilesheet just won't change no matter what. Sometimes when you change one tile, it changes a seemingly random number of tiles to the right of it to the same thing. Sometimes if you do a square selection and try to mass change them, it offsets the select and doesn't change the top row, but changes the row beneath the selection.
I can't pinpoint when this happens or why, but it's an extremely frustrating bug.
EDIT: Ok! I think I've figured out what's causing all the problems. If you're in square selection mode, the whole process of switching inbetween 4 and 8 bit get's all messed up. But, if you're in normal selection mode, it works perfectly fine.