Just out of curiousity, how come you're using Capture Now versus like a batch/clip capture? Can you elaborate on the problem? Is it happening even if you try and catpure only a 5 sec clip or is it happening only when you're trying to capture 20 min clips?
I'd start by trashing my preferences and seeing if that will do anything for you. I wouldn't think so from your description, but hey, I'd at least try it.
Next, are you sure your FCP capture settings properly reflect the input settings from whatever device/tape format you are attempting to digitize from?
Is FCP crashing, or is it freezing up? I had the problem of it freezing up before I realized that your clip has to be rolling before you press Capture Now. I was just pressing Capture Now and expecting that to start the playback device. Works great for me now.
Varicam - I sometimes capture an entire tape, or an entire interview, so rather than set in and out points at the beginning and end of the tape, I use capture now and let it do its thing while I'm doing something else.