No what is happening is you are getting time code brakes. and FCP is smart enough to work around those brakes and cut it out. So you might be lossing one or two frames but they are the frames that have the brake in them. So when this happens batch capture makes a new clip and keeps going.
To prevent future problems, try recording black onto your tapes before taping. This creates a continues timecode. I started doing this after I ran into some problems with batch capturing as well.
Shooting with a DVX? after each record......when youve played through your footage make sure you hit the rec chk button or just hit it straight after you stop recodring if you are not going to review it. That will que you up to a frame in your tinecode..... thus avoiding breaks... takes about four seconds to do and saves a lot longet in headaches.