We are learning this stuff by using the 'hammer to the head' method...
Premiere CS5 to After Effects CS5 'replace with after effects composition' method loses the trasitions that were placed in Premiere. They don't show in the After Effects composition. Fine.
So, doing the all the effects and Magic Bullet effects in the footage and then doing a multi-machine render to a PNG sequence is fine. Then, instead of using Media Encoder to assemble the PNG footage back to an AVI to re-import to Premiere, it's FAR faster to have after effects re-assemble the PNG to an AVI. Here's where the 'weirdness' comes in. We import the newly assembled AVI-PNG sequence to Premiere and CAN"T ADD transitions to the AVI file. We will put in the cuts where we want it and it doesn't work! HUH? Here's where things go really sideways...If we assemble the same PNG sequence using the ultra-slow Media encoder, we can then do transitions in Premiere. WHAT! I don't get it. What is After effects doing differently than Media encoder to put it all back together?
Sorry for the 'frustration', but man, what is goin on?
Thanks again for everyone's time.
See my reply in your other thread. Re-reading this post I do get the impression, though, that you are messing up the frame rates somehow and thus run into problems...