Has anyone else ever seen this happen? It's only happened in CS5, and we're witnessing it happen almost every day. I'd guess that there's something weird going on with the Avid1:1x codec, but we use the exact same codec in CS4 without issue.
This may relate to the inability to access the CoDec specific settings panels for Avid CoDecs and specifics. I would dare a bet and say that the CoDec is locked into a specific framerate that isn't compliant with your comp settings. here's the deal: Since Avid CoDecs have dedicated settings for fields, it seems to me that when rendering at half res it is interpretting AE's reduced res as fields, which it thne simply duplicates or as correct full frames. At full res, it interprets the data wrongly and thus you end up with incorrect frame counts. So, to cut a long story short, unless you get access to the CoDec options from wuithin AE, which because of the mentioned bug may not be possible, I see no way to get it working correctly. Thus, for the time being, you will have to use otehr CoDecs or image sequences.
I did a bunch of troubleshooting with Paul Uusitalo at Adobe, and it looks like the bug is actually in QuickTime Player -- it reports the wrong frame count. No idea why, since everything checks out (QT reports the right frame rate, so that's not the issue), but every other program we tested the clips in reported the correct frame rate.