The "Update Firmware" process loads the firmware in the order you see the modules displayed in the loader tab, top to bottom. That said, in my experience there seems to be some dependencies across modules, but I've only really experienced that when fooling around with various module versions that aren't apart of the same firmware package.
Do you have any blinking lights on the dash?
Try disconnecting the low voltage plug on the top left side of the battery for about 10-15 minutes and then plug it back in. On the A pack it's the black screw-on connected behind the left side shroud.