Here are a couple of thoughts:
1.) can you disconnect the Matrox and test the files in a non-Matrox Project? Any better?
2.) as PrPro can have issues with MPEG files, can you Export as a DV-AVI (or similar) from your DR-HD100? Any better?
3.) can you demux your files into elemental streams and Import these separately?
4.) is your OOS issue constant, over the course of a Clip, or does it drift? Constant can be easily fixed in PrPro, by turning Snap OFF, then Alt-clicking the Audio only, and nudging it along the Timeline. Once done, the Audio and Video will be re-linked. Rember to turn Snap back ON. If it drifts, you may need to Razor the Clips and work on the resulting parts separately, as stated before.
5.) have you tried Render/Replace for the Audio? This will get you a WAV file. Is that any better?
CS4 solves this problem. I have had no issues importing the same files that were out of sync in CS3 into CS4. In CS4 the same clips were now in sync.
That is good news. Glad that CS4 did it for you and thanks for reporting.