I'm seeing a similar issue in the opposite direction. When connected to USB I am seeing voltage on Vin.
Yep, I see exactly the same thing. I have a high-current draw external load (HL1606 LED strip) that I'm powering with an external 5V PSU, which also supplies 5V to Vin. If I forget and disconnect the PSU whilst leaving the USB cable connected, the Vin pin supplies 5V back out to the LED strip, but it can't supply the current needed (up to 2A), and the strip goes haywire. I haven't toasted my Duemilanove yet, but trying to draw 2A from it clearly isn't a good idea. Seems like a design flaw to me.