Soundtrack Pro corrupting audio files during editing

Using S'trackPro 1.1 on both G5s and Mac Pros, I've experienced a recurring issue when editing long audio files (16bit 48Khz aiffs of 60-120 min durations).
Import files directly in Audio File edit mode, usually apply a limiter and/or normalize and save with new file name. I often find as I move around the waveform to preview results, the playback stops responding accurately, playing the wrong part of the file randomly.
Once saved, the file seems to have random "splurts" of audio appear in inappropriate places throughout. For example, a 2 sec "splurt" from the middle of a 120 min file may appear 10 minutes before the end, seemingly at random.
It's odd that I've experienced this on numerous machines, all with quite different specs.
Any suggestions appreciated.
3 x G5 Dual 2Ghx 2.5Gb RAM, Mac Pro Quad 2.66 5Gb RAM   Mac OS X (10.4.9)  

I actually use the 'save as' function that consolidates all the audio clips and move them onto a separate drive. I'm doing a lot of large projects that have more clips than are actually used. Consolidation means I can move and work on another machine. And in the end it's easier to archive this single directory of files. Works for me, especially because sometimes the audio sources are scattered in too many places on my system.

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