I just hooked my mega board using a 9v power supply connected to the vIn and ground. In the course of troubleshooting something in the circuit I noticed that instead of the expected 5v the mega's 5v pin is outputting 9v. After some testing it seems the 5v pin is just passing through whatever voltage is being supplied to the vIn. The 3.3v pin is still outputting the proper voltage. The digital io pins also seems to be putting out 9v as well.
Stop powering it through vin immediately. Regulator has failed, and as you sispected is just passing the input voltage through to the output. You have probably damaged the chip running it like that.
Thanks that was my diagnosis as well. Thanks for confirming my suspicions.