Once the program is installed, start it and click on the Advanced Tab. For now, just make sure that the only check mark is beside the Final Cut Program and then click on the "trash selected items" icon at the bottom of the window. Now when you start FCP it will have a new set of preference files. Later, you'll be able to configure FCP to your liking, save those prefs. with Preference Manager and when FCP starts acting weird again you can trash prefs and then use your back up prefs saved in Preference Manager.
Anyway, make sure that you've got a good firewire connection between your computer and video deck (XL2?) If you've been dropping frames during capture then either the connection is sketchy, the tape transport of your camera/deck has issues, or FCP prefs are corrupted. Don't turn off "Warn of dropped frames during capture." You need this turned on to make sure everything's capturing properly. Turn it off and you're going to get clip mismatch issues like you're experiencing now.
i think you can also get those same dropped frame errors if the hard drive you are capturing to is having problems.
Ensure you have a drive capable of 7200rpm, and also do not capture to the system drive if you can avoid it. Last time i checked, USB drives are not recommended either because they write data in bursts (packets) rather than as continuous data streams such as in firewire.
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