WXM,
You can shift the picture up and down with BT8x8 Tweaker for VirtualDub: http://www.doom9.org/index.html?/capture/bt_tweaker.html
If you are using another program to capture, you can try running VirtualDub at the same time. When you start a capture, regardless of the the software in use, the border settings are reset to the default values. To apply your changes again, press the Reassert button in BT8x8 Tweaker.