I'm having a problem with TMPGEnc 2.5 Pro. After I export the lossless AVI from After Effects, I put it into TMPGEnc to convert it to a DVD compatible mpeg. It does this fine, but at 8:02 to 8:03 the sound cuts out completely, otherwise it's completely fine. I changed a setting and the sound cuts out from 8:01 to 8:02 now.
Why are you processing audio and video at the same time? You're much better off saving the audio to a different file in AE and converting it separately.