This appears to be a common issue. I was having subtitles syncing issues and another poster here came with a whole long procedure to address the issue which involves comparing the run time in Encore vs the run time elsewhere (he was using MediaInfo, I just looked at it in Premiere) and adjusting the subtitles accordingly. No idea as to the why, but the workaround works. That said, i've never noticed the issue except for with subtitles. The audio matched.
And it is so awesome that this and Encores other buggy ness will never be fixed.