Some of the reason we were given good seats for the second show are probably that it had been raining/storming for so long that a lot of people with FPP's for either show had probably gone home, plus we asked within a few minutes before the show was about to start, so they could see there were still plenty of empty seats (and we were wearing our anniversary buttons - not sure if that helps too!). I'm guessing for clear nights (if we ever have any!) they wouldn't have the same availability.
However, there was lots of confusion probably as to what protocol was since this was the first night they'd had the rainout. As Hiro posted from me above, different CM's told us different things. Heck, Touring Plans (not random people but Touring Plans itself) was posting the next day that your FPP's for JB would be honored for 4 days. That was quickly rescinded. Our "special" FPP didn't appear until well after the show, which I think caused some of the confusion for CM's too. I'm assuming they'll figure out a set routine soon, especially if at least one show a night is rained out like has been happening!
While I agree it's disappointing that the FPP is good for pretty much everything BUT the JB show again, you have to admit it's kind of cool to be able to grab another Soarin' or A&E or 7 Dwarves the next day in whatever park you're in!