I downloaded MPLAB-X 1.3 this afternoon, and had another go at Proteus.
It seems to be working better than 1.2 did.
It's still a bit flakey, but I was able to get a simulation running.

In your .dsn, try setting the Program File in the properties for the PIC chip to the .cof file.
The .cof file is in ... your MPLAB-X project \dist\default\debug
Then save the .dsn

Press the debug button in MPLAB-X.
Let me know if that runs.
I don't know if that's what got it to run or not because there were so many things I tried.
That's the last thing I remember changing.