I just upgraded to CS4 and cannot get the output to work. I started with a project in AECS4 and rendered it. I brought it into PPCS4 and cut some music to it. When I go to output-media, the encoder comes up saying it cannot read from the source. So I tried adding the project into the encoder and it says "Cannot input file" which is a PPCS4 FILE. I would appreciate any insight.

When you say you 'brought it in' did you render out of AE then imported in the media or did you use Dynamic Link? If you rendered out of AE, what settings etc did you render to?
Have you tried to DL the project into PP.

In AECS4 I rendered the project to .avi and loaded to PPCS4 through the Import File link. The project played back well when I was editing the music. It just won't encode out of PPCS4.

Strange. I've never had that happen to me. Can you try to using Dynamic Link in Premiere to link to your AE project and see if that works.