Three months late, but this just happened to me as well - anyone still need info on this?
This will only apply (I *think*) to you if you get a "breaks in the timecode" message after you finish capturing.
I found that if the timecode (TC) is not consistent throughout the tape, and you capture through the TC discrepencies, the timecode at later points in the captured video will be relative to the TC where you started capturing, and will not be the actual TC on the tape.
EXAMPLE 1: there's breaks in the tape between shots, where there's no timecode at all. you set FCP to record through these breaks. on the tape, if there's a break in timecode, the next shot will start at 00:00:00;00. but on your system, the timecode at that point will not say zero, will instead say a TC relative to the point you started capturing at.
EXAMPLE: our footage was shot on 3 cameras using external TC generators. so wherever the tape stops rolling, the external TCGEN keeps going. So when the camera starts rolling again the TC starts at a later number. Trying to capture the entire tape from this was frustrating, because the timecode of captured material was not the correct timecode. It was always at a linear point in time relative to the TC at the in point of the capture.
SOLUTION: go to user prefs. go to where it says "On timecode break:". the default setting is "warn after capture". change this setting to "make new clip". this will take much longer to capture, but the TC will be correct.