I captured some recent footage shot with my Canon XL2 and noticed that the audio gradually went out of sync from the video on the captured clips. When I control-click on the clip and check the item properties, I noticed that the Audio rate under "format" is 48002hz (as opposed to 48Khz) and on another clip, it was 48007hz. What is happening?

It's a documented firewire issue - Nothing to do with audio properties of the QuickTime.

1) Make sure tape has no timecode breaks
2) Use a deck to playbacks to capture card (best way- also can capture to pro-res)
3) Capture your tape in 25 minute chunks via firewire

-C