It appears, since you can still disarm the system with the PIN and t/signal switches, that your fob's are no longer paired or assigned to the module. If that is the case, I'm pretty certain you will have to get a dealership to reassign the fob's using the Digital Technician equipment. If anyone has the '07 or later Electrical manual, perhaps they could check to see if it lists any other way to assign security fob's. The old button system allowed an owner to assign fob's, but the only info I've seen on the new system makes it appear that the DT is required (see attachment).
BTW, the next time you want to disconnect battery power, you need to disarm the system before removing the maxi fuse or disconnecting the battery cable. With the fob present, turn the ignition switch on and leave it on while you disconnect battery power. It appears that the presence of the fob alone doesn't disarm the system, you also have to turn on the ignition. From your original post it sounds like you didn't do this, and the alarm thought an unauthorized thief had cut the battery cable. That's why the alarm has it's own internal battery, btw, so it can still sound the alarm if the battery cable is cut or removed. I'm wondering if this removal of main battery power while the alarm was still armed isn't what has created your current problem. I'm guessing yes, but can't say that for certain.
Jerry