Thanks for the reply Joseph. That’s what we’ve ended up doing: exporting a high res file out of AE (Animation .mov in our case), then using Media Encoder to batch the file types we need.
I’m guessing/assuming that the fade-up has something to do with mpeg 2 and that dynamic link to After Effects. I’ve never seen that before either, and it couldn’t be reproduced with another codec: h.264, etc. That combination just doesn’t work well. Strangely though, that fade from black effect only affected certain layers. I have a lower third on this spot, and the lower third didn’t fade up like the rest of the video; it was perfectly normal. Even if I created a new composition in AE with only one layer (he master comp) and exported that, I got the same results. Weird right?
Anyway, no harm no foul. We’re getting the spots out now. but any bug/glitch/whatever is always worth noting…