I had constant sinchronization issues during the transfer of files from PremProCS5.5 to Encore. At first I thought it to be an Encore issue but through experimentation found it was in PremPro. I had asked for help in the Encore forum but no one had advice that seemed to help with this issue. This seems to an issue with a lot of users. It turns out to be an easy fix if this pertains to you.
Often, I add to the beginning of the sequence in PPro, a title crawl or still. I usually need to start the audio a few seconds or frames in from the beginning so there is a gap that has nothing in it. The audio is always "linked" and "grouped" and is in perfect sinc before sending it to Encore. After making the DVD I found the audio to be consitantly a few frames out of sinc with the visuals. On spec I took a section of audio (any section) that was equal in size to the space and placed it in...thus filling the gap. Naturally that piece of audio had the level placed to zero... and voila. For some reason PremPro needs to have that gap filled or it will shift slightly during the transition.
On the internet tons of people have this issue with PremPro so hopefully this will help someone else. Cheers