This is a known bug, and there's no known remedy. I believe it's due to limitations in how the plugin gets track time from WinAMP, but I could be mis-remembering. Look at some of the SYLT threads (or do a search if you can't find them) for Patrick's explanation of the whole thing.

Incidentally, I *believe* that the timestamps are, in actuality, in sync with the song as you tag it, but it's just how it "appears" in the plugin that's wrong. Again, it's been awhile and I've been distracted lately, so maybe that's wrong. Before giving up on SYLT entirely, I'd sync over at least a few test tracks to make sure it's as bad as you think it is when emphatic displays it.

Also, adding a negative offset in the SYLT config will have the lyrics start to scroll in a little early, which should help if things are really bad. I realize these aren't ideal solutions, but I'm just trying to provide alternatives.