Yes, I too have found that the "Pro Panorama mode" does not play nicely with the other capabilities. It seems bolted onto the firmware, not integrated. I wasn't entirely sure what was going on over the weekend, but your comments hit home.
So far I've done a fair amount of shooting with both EXR auto and regular raw mode. I haven't really worked out the differences, although it is entirely accurate to say that I like some EXR results better and some RAF results better.
_____ Brian... a bicoastal Nikonian and Team Member
My gallery is online. Comments and critique welcomed any time!