Just to add my experience:
Rendering from Adobe Media Encoder will not help running video 100% synced on iPad2 or iPhone4s [devices I’ve tried].
I’ve experienced even worse problem: Default HD image created in Photoshop [as PSD file] and imported in AE is set to 30fps project. When open this project and export as 29.97 – I will get half frame on 3-4 times in 3 minutes video so instead removing layer in some part of the video I will get half transparent layer. It looks like a flick or error while playing video, but when load video back to Photoshop and zoom to that frame on Photoshop’s video time-line – I will clearly view transparent layers instead 100% visible or 100% invisible.
I’ve rendered final video in my old way – from AE directly 🙂