Ah, sorry about being unclear there: the 3,4,5 was to indicate that I’ve had the same problem with each version of After Effects and Premiere, I’ve never had them all installed simultaneously.
This isn’t a problem with which audio I use: I’ve tested with multiple files, whether it’s compressed audio being imported or raw, there’s no issue with sync inside AE. The problem only arises when I’ve exported the Quicktime file, and then, the problem is only in the Quicktime application.