I have this issue also. Since I’ve had my Kona 2 card longer than I’ve been working with DVCProHD, I didn’t think that the driver could be the culprit. Interesting. I have all the latest updates, and it doesn’t seem to be an issue with that. I had assumed the shift was coming in the YUV to RGB conversion (since AE only works in RGB AFAIK).
Here’s how I’ve been dealing with it until I find a solution: Export the prtions of DVCProHD material you need for AE in FCP (which as you know, handles the footage corectly.) with Animation codec, or Uncompressed. Bring that in to AE and then render out with Animation or UNC back to FCP. Lots of extra rendering, but it gets the job done.
Depending on how much footage comes from AE in an FCP sequence, sometimes I’ll just bump the entire FCP seq to Uncompressed and use that as my master sequence.
Please keep us posted if you make any progress towards a REAL DVCPro HD solution though! I have seen this come up several times now without any proper solution.