I have seen the same thing, when using converted MPEG-2 files (converted to DV-AVI Type II in DigitalMedia Converter). Everything was perfect in PrPro, and even when I Imported the edited DV-AVI's into Encore. When Burned to DVD, several scenes had OOS issues. I "fixed" these over and over in PrPro, but could NOT get them to Burn properly - regardless. I chalked it up to the original source files, and/or DMC's conversion. However, it's conversions from all sorts of crap are usually 100%, with no OOS problems. These just gave me fits, and I finally had to tell the client, that unless we could get to the original source files, what you see is "as good as it gets."
In my case, I even tried to "guesstamate" the OOS, as I could not see/hear it in PrPro and Encore. Just flat did not work. Most Clips were perfect, but some would flat not sync, regardless. Lot of work, and wasted time, and never seemed to even get closer to sync in these few Clips. Why? Have no clue, as all the rest (same footage, format, CODEC, etc.) synced up fine. Very frustrating, but that can be the nature of the beast, when working with non DV-AVI material sometimes.
Good luck on this, and sorry that I do not have an answer for you. Though too late for my Project, if you ever do get it nailed down with some fix, or workaround, please post. I'm curious.
>"get it all sync'd to the exact milisecond"
How on earth somebody is able to that is a big wonder of mine (except for if they use 1000 fps though).
Anyway, there's more between heaven and earth than anywhere else, so...
I have also have had some cases of "funny" un-sync'ed cases, well, actually not that "funny" if I think about the source footage.
My solution has been to treat video and audio separate, one conversion of the video (to uncomressed avi or mov) with one program, and the conversion of the audio with another program (PS! Never used Super for anything btw), and then joined audio and video up again in Premiere.
It mite be rite, and it has solved my problems, but it could as well be wrong for your footage, but maybe worth a try.
PPS! Judging sync inside Premier is one thing I don't do too much, except for visually (waveform compared to picture, not playback).