I'm at a loss as to how a simple jump (*done properly*) could have blown the ECU, unless it were jumped from a 24V source found in some military and industrial vehicles. I could also see it happening if it were hooked up backwards, but taking damage like that would(should?) have rendered the vehicle entirely useless.
Perhaps the battery was only "mostly" dead, and the ECU (or relevant module) was only getting enough power to only partially finish any register operations (I've run across similar when programming AVR/BS/PIC microcontrollers)? Voltage drop has a strange effect on little computers.
I'd disconnect the battery completely for 10 minutes or so, and see if that resets the electronics.
Badger: A-Team quote FTW
