You shouldn't really be experiencing frame drops with your setup - would you know the rating of your harddrives? i.e the spin speed of the disc (it'll probably be 5400 or 7200).
Have you tried capturing to both drives - you may find that one is faster than the other. You might also want to defragment both drives to speed things up a bit (but that's clutching at straws!)
Try using a freeware app for DV capture - Pinnacle Studio is reknowned for hogging system resources. There's a few links to cut down programmes in this thread http://www.videoeditingforums.co.uk/viewtopic.php?t=10 (at the bottom)