Either because I can't give up that easy or because I'm lazy and hate sending things back, I kept looking for a solution. It looks like reinstalling the Mega2560 drivers fixes this problem. You might file it away somewhere in your brain for later.
To update driver for Mega 2560 for Vista:
- Download Arduino IDE v21 (unpackage)
- Plug in Mega 2560
- Right-click on 'My Computer' and select properties
- Select 'Device Manager'
- Scroll down to ports
- Find the port the Mega 2560 is connected on and right-click and select properties
- Select 'Update driver'
- Select 'Browse my computer for driver software'
- Browse to the folder where you unpackaged Arduino IDE v21 and select the driver folder
- Press Next
(From here it should find the drivers and install them correctly... if not I'm at a loss, you'll have to find someone smarter)