Robin,
Yesterday I finished my first major project using 5. (Woohoo!) I had a movie from AE in there with an alpha channel and it worked as always. Because my project was 8bit uncompressed I had to render the files, but they were very clean.
My render settings from AE were Animation, millions+ and I set the alpha channel to straight.
Check to see if yours are premultiplied, could be the problem.
No problems in the same project with transparency on about 25 PS layers either.