I do a lot of dynamic linking between PrP and AE on a PC (HPZ820). I can tell you that in CS6 it is MUCH more stable.
Malcolm, try this workflow and see if it helps.
1. Cut in PrP
2. Select clip on TL and send to AE as DL
3. Work on comp in AE.Save.
4. Check in PrP. Render in PrP if needed to view.
5. Refine back in AE. When satisfied, I export as DNxHD making sure I check “Project Link” in the AE export queue dialog box.
6. I import into PrP and replace the DL version of the clip on the timeline with the DNxHD movie.
7. If I need to change thing, I select clip and right click. Then select “Edit Original”. Boom, the AE project opens and I make revisions.
Also it might be a good idea to delete all your Media Cache and Preview files in their respective folders, just to clear out old junk that might be screwing things up. Then open PrP and try this flow out.
Tom Daigon
PrP / After Effects Editor
HP Z820 Dual 2687
64GB ram
Dulce DQg2 16TB raid
http://www.hdshotsandcuts.com