I should probably just order a new one, but my maker-spirit makes me want to fix.
I accidentally turned on my bench supply cranked up to 10v. The xprotolab went black.
I examined it, and the 3v regulator was clearly crispy, so I removed, and applied 3.3v directly, and it came back up.
I ordered some regulators, and replaced it today. 
It works, kindof:
1. Display seems fine, menus, etc.
2. Looking at a known signal, the magnitude seems wrong/amplified. e.g. a 0-5v signal shows offset by several volts.
3. AWG output is diminished, and well, not right. sine waves are clipped, and everything is in the 1v peak to peak range. (verified with another scope)
4. It doesn't show up as a usb device when I plug it in (Windows even as an unknown device.)
 
I haven't tried re-flashing it (I have an avrispmkII). I also noticed the opamp, so I ordered a few of those in case I have to replace.  I'm not an EE, but there also appears to be a bias voltage or something in the schematics, which may be why I am getting the offsets, but don't have a clue about how it is generated.
 
*UPDATE* I did reflash it with 2.17. No appreciable change.
I also noticed that D1 (which appears to be the voltage reference I mentioned above. gets very hot, and looks a little burnt. Too bad I didn't notice that before. I'll have to wait for my next digikey order.
 

Hi. The voltage inverter chip (U4: TPS60403) is probably damaged as well. Check if the negative 5V pin has indeed -5V./\r\n/The chip is behind the display, to replace the chip you will need to cut the double sided tape under the display. Do not try to lift the display because it will break it. To cut the double sided tape do as following: Using a small jeweler?s flathead screwdriver, reach under the display and apply a sideway motion to cut thru the double sided tape. You can fit the screwdriver between the K1 and K2 buttons, and then between the K2 and K3 buttons. Once the tape is cut, or mostly cut, you can try lifting the display, but you must use little force.