I had this same problem with DV50 and an AJ-SD93. I actually found the answer here on the COW in the archives.
My solution was to batch capture (just one large clip in my case) instead of “Capture Now”. For some reason, actually marking the in and out points for the clip forced FCP to use the correct sample rate for the clip.
I would bet you that either way, the capture was just fine. Just something got screwed-up in the metadata of the file that told Quicktime the wrong sample rate.
Is there a utility out there to edit Quicktime metadata without changing the data contents of the file? Like pixel aspect data or anamorphic?