So I need to import my lip movements on a character. The lips are already perfectly aligned. However, when I import them, they bounce all over the place for where they load for some reason. Even if I import the exact same thing twice for two different lip poses, i will still have it imported just randomly so it doesn't even sync with its self when using the same image.

Is there some way to fix this? It is such a tedious process trying to align it because you have to go in and out of the character editing mode just to see how it lines up in motion, which is silly since if it just imported the files in the same spot, they'd already be perfectly in motion.

When you import the mouth shapes, are you loading them into the mouth Sprite portion of the composer window?  They should line up with that sprite.   If not you can use the math windows to center them.   I've had to do this with my projects.   One lineup is generally ask you need.