One thing I have done in the past if I have not already started cutting the clips is to export a batch list of the problem clips and reimport it. Then capture. It seems that exporting a batch list cleans some of the bad data from the clips somehow. If you have a sequence that these bad clips link to, you could try exporting and EDL and recapturing that way.
How many tracks of audio per clip do you have? I have found that Soundtrack does not support more than 2 audio tracks. Also, it does not work with merged clips or nests. Is this what you have?
Have you tried to callibrate the Frame offset? When I first got the Io, I had to set it to almost 12 frames. Do you always playback with an external monitor?
Sadly, when you upgrade to QT 7, you lose the ability to export MPEG 2 files via QT. They expect you to use DSP or Compressor. I think that error is some weird way of tell you to use compressor instead. but maybe I’m wrong?
Try reinstalling quicktime. Just download the latest Quicktime and install it over itself. I have found on other forums that when people upgrade they lose their firewire connection but then Reinstalling QT must rewrite a missing file or something because it generally works.