AE CS5.5 (Win x64) will not read Avid DNxHD MOV files produced by the BlackMagic Design Hyperdeck Shuttle 2. All other software, including Bridge and Premiere Pro CS5.5 read the files fine. If I re-wrap the file with ffmbc and the only change is to reduce the 16 audio tracks (14 empty) to 2 or one, AE reads the file fine. PPro CS5 had a similar issue, which was fixed in the revision to CS5.5. See this thread from the Premiere Pro forum:
http://forums.adobe.com/message/3888889
AE and PPro CS5.5 have two different versions/file dates of the Quicktime importer file (ImporterQT.prm), so the issue may have just been missed with AE.