Good point, I hadn't had a flat battery at the time - it does sound like diagnostics are his only real way forward at this point as something isn't working properly.
I had the same kind of issue when I first bought mine with the RF keeping BECM awake and all that - However when I entered my EKA, all the locks popped up and it let me resync the key and start the vehicle. I wonder if his BECM as gone into lockout which is preventing him from getting it going...
I can't see his location on his profile anywhere, but if he's local to me I'm happy to go have a look with the Nanocom and/or BECM programming gear...
Problem with flat battery after locking with Fob, is that with a flat battery when you unlock with key BECM doesn't know about it. No power. So when you reconnect battery all it knows is car is unlocked and shouldn't be. Hence alarm.