I have recently had a similar problem when on FCP, running off an xSan raid, with an SD 8bit Uncompressed sequence. The sync would sometimes be fine and sometimes not, depending on what the system felt like doing. The same clip could be in sync one time and not another. I concluded that the system couldn’t keep up, but couldn’t be sure whether it was the raid or the card or the Operating System or FCP that was the problem.
To investigate whether it is due to the raid, I’d suggest running a test which I didn’t have chance to do: Try playing out when no-one else is connected to the raid. Also be sure to disconnect all other network cables/access (internet or non-media networks). A colleague and I have a (completely untested) theory that excess network traffic slows down the effective speed of the San (and not because of media throughput limits). (Theory is: Although the media throughput capacity might be plenty high enough, if the metadata traffic that oversees the media data flow isn’t getting processed fact enough, then the media data flow will get delayed.)
However, what is bizarre is you seem to be saying that if you export a quicktime and play it on someone else’s (high spec) mac/pc, then it is still out of sync? And to confirm, to create the quicktimes you are exporting? – you aren’t playing out through the Kona to a hardware encoder? And when you play back the quicktimes on another computer, it is playing them either off a local drive or a different harddrive/raid that is NOT the HUGE raid you are using? If both those assumptions are correct, then I’m stumped as to what’s causing the trouble. It suggests it’s unlikely to be an issue of either media drive speed or the Kona card’s processing speed. Can only guess that there’s some sort of file corruption going on somewhere??? Or that FCP is being exceedingly retarded – but no idea why.
Just to confirm, you say it was filmed on HD – you mean eg. HD Cam or DVCPro HD cf. HDV? (HDV seems to have all sorts of fun issues due to it’s interframe compression that might explain the problem.)