Using Avid Media Composer 3.5.4 on a certified HP xw8600 workstation. I have a :45 piece in 1080i that has video and an animation created in AE. I export the spot as a .mov file with the animation codec. I can see the spot in Quicktime when done.
My problem is trying to convert the QT file to MPEG4 in Adobe Media Encoder. I have some custom settings, but for some reason, the MPEG4 files goes black during the AE animation part of the spot. Audio is still there and video plays back fine as well.
This won't fix your issue but Adobe Media Encoder is generally considered to be a pretty poor encoding application...often producing just plain weird results. We've never gotten it to work properly through many, many Adobe versions with Premiere and AE.
My suggestion is to use the freebie Handbrake to make your mp4 files. It's excellent, is fairly easy to use and best of all...is free and available for every major computer platform.