The .txt or .srt files should tell you the precise timecodes. Compare them to your Encore timeline. Do they match?
What file format did you import to Encore? mpg? Encore "prefers" demuxed (m2v and wav/a3c). If you brought in mpg, Encore will probably retranscode them, and that can move gops and introduce sync problems. Upon import, what does Encore show in the DVD Transcode status column?