Sorry for not posting my final findings.
Adam, when the files were not corrupt, they where not well liked. The guy that set up the encoder was making everything 720×406 and some had 4 channels of audio. Premiere didn’t like this very much. I keep asking for normal video resolutions and not getting them. Finally after weeks of the home office calling Adobe and them trying all type of things, countless reinstalls, only a single sequence in a project, total workflow busters, they changed the resolution to 720×480 and all is fine. Rock solid.
While I still like FCP better, it would not work for this workflow at all, I have to say PP to Media Encoder is AWESOME! The smoothness of integration is get the start. The fact that there is no link between PP and Media Encoder once the file is received makes it so much more usable.
I just need to totally remap the keyboard to what I’m familiar with and it will be golden.