Just guessing and/or thinking out loud because I've really no idea what might cause this.
Try checking and cleanig the connection from your firewire cable, both ends. Also, if you can, try a different lead to see if it helps.
Run a tape head cleaner through your camera before capturing just to make sure it's all clean in there as well.
Other than that, all I'm left with is the normal 'make sure your HDD is well defragged' as many a cpature issue has been resolved by creating extra space and defragging.