The fact that it is out of sync in your capture scratch quick time files leads me to believe that it is indeed a settings problem. As other people asked is it the same amount of slip through-out the clip or does it get worse and worse as the clip goes on.

I have also seen that the computer can not keep up with both at the same time on longer captures because its too processor intensive, what is the clock speed of your G5? If its one of the single core slower models then you may want to limit your capture to 20 minute intervals.