I experienced this same problem on a system with Kona LHe card especially when editing 720 59.94 sequences. When I searched, I found lots of similar experiences with that card.
I followed lots of leads to improve this, in my case the thing that helped the most was getting the correct RAM configuration in the Mac Pro. There are a very specific directions as to how pairs of RAM are to be placed in the risers in a Mac Pro. Turns out I has misread them and was running with a less that optimum setup.
However it would seem from the frequency of posts, that the LHe card is especially sensitive to sync playback problems. I've never read that a solid fix has been arrived at. I still occasionally see the problem after my RAM fix.
Typically the sync of playback will go out after doing edits in the timeline and then playing through a section that has unrendered clips. Usually pausing for an instant then playing will cause it to catch up. If it is still out, I'll load any other sequence into the timeline, then switch back to the first one and the problem will be cured for a while. It's as if forcing FCP to rebuild its buffers clears things up for a while.
With everything rendered I don't experience the problem.
I've never experience this problem with my other system that has a Kona 3 card. Both are Mac Pros, with SATA RAIDs, 8 to 16 gigs RAM, Leopard.