So, I’ve found something that worked for me:
My project was shot with 2k and 4k files.
In Premiere I was selecting ‘scale to frame size’ on all the clips…. this seems to make all the clips into its own ‘precomped’ clip when you copy over to AE and so the actual clips aren’t reading all the speed/duration data, it’s this precomp that is and the clips are staying unaffected/confused.
My explanation is terrible, but the answer that worked for me is:
Uncheck ‘scale to frame size’ before copying over.
Hopefully that works for someone else too!
Best,
Charlie.