I just upgraded from Premiere 5 to 5.5. Dynamic link files that worked in a Premiere 5 project are not letting the alpha channel work from the AE comps in Premiere 5.5. Any ideas for a fix?
Did you update to 5.5.1? Read here: Adobe Premiere Pro CS5.5 (5.5.1) update: bug fixes, including some for Mac OSX v10.7 (Lion) compatibility « Premiere Pro work area
One of the bug fixes:
If an After Effects composition with a background color other than black was included in a sequence and Mercury Playback GPU Acceleration was enabled, the alpha channel transparency of the composition was ignored.
Download links are available in the post above; I don't believe it's available via Help > Updates yet (but you can check).