Thanks for this James,
The USB's 5v isn't being disconnected. When I connect just a 12volt battery to Ramps, it pipes 12 volts through the Vin pin on the Arduino, but the 2560 will not turn on. If I then hook up a USB cable, the 2560 will come to life. (It will do that even without the 12 volts). The Ramps shield drives stepper motors and it requires at least 12 volts to operate. Normally, I'd just hook a 12volt car battery to the Ramps power input, and both it and the Arduino would work fine. Now, I have to have the 12 volts hooked up to Ramps for it to run, AND, a USB cable to power the 2560. Otherwise, only the fan on the Ramps will turn on, and it's connected directly to the 12 volt supply.
Do you happen to have a component layout for Mega 2560 R3? I have seen a picture with the componets labeled, but it doesn't match mine exactly. The part that looks like a 5 volt regulator looks like maybe "AMS ?17", and I can see 5.0 stamped below that on it. I think it may even be showing signs of a burn in the center, but it's hard to tell. If it is a 5 volt regulator, do you know where I'd find a replacement for something like that?