I've experienced this on a number of FCP stations... currently a MacPro running 7.0.3 with AJA IOExpress with driver 8.1.1.
DVCPHD 1080/50i source. Editorial cut... few effects (guide titles and speed changes), lots of audio tracks. 75min film broken in 3 (to avoid memory issues when manipulating full film).
1. Sync is off after the sequence tries to play through a section of video it can't render at full res (e.g. boris title with drop shadow, or apple title with cropped semi-opaque cropped slug behind for subtitle - Running unlimited RT with 'warn drop frames' off).
I assume this is normal behaviour (i.e. it's dropped some video frames and doesn't/can't regain audio sync) but would like this confirmed by others, any neat workarounds you may have gratefully accepted.
2. While editing, playing part of sequence sometimes results in sync errors. Stop/Play cures this. This is the more annoying problem as it is inconsistent. I've read elsewhere that this may be due to blank sections on V1 - and this would be consistent with the errors.
Fully rendered timeline plays back in sync for 75 mins without a problem, so I would think that would discount any disk read speed issues.