I posted the issue a while back, and ended up having the issue resolve itself. However, it has returned and I need a quick solution. I have a project that is fully transcoded and in one spot, the audio doesnt match. I've verified that the Premiere Project is fine, so this must be happening between the link with Premiere and Encore. I'm using CS5.5 as well.
Please help me, I've relinked everything and I have tried to retranscode everything with no luck.