So, after posting my OP in the "Contact Us" portion of the web page -which works now, I almost immediately got a call back from one of the senior shop employees who had a meeting with the owner to discuss my issues.
1) It is shop policy to only fill with Nitrox tanks that have nitrox bands. I explained that I understood shop policy and would rather take the tanks somewhere else to fill than have an employee violate their policy. This person also stated that it was Alabama law that Nitrox tanks have the Green/Yellow band (I sense B.S. unless he's talking about shop tanks). However, the shop policy has been amended to allow the filling of personal tanks with a Nitrox VIP sticker. The newly trained blenders have been counseled in this change. Also, they agree that there is no excuse that my tanks were not ready after two weeks. I was offered free nitrox fills/air cards upon my next visit.
2) the shop will no longer promote inshore sites, as there are only 3 diveable sites within 9 miles of Perdido Pass (their words, not mine). If someone asks, they'll still schedule a trip there, but for the season, if you book a trip, it will be offshore (which generally promises better viability, and a greater selection).
3) There was lots of explaining about the seasonal employees, and the inability to have enough staff available, etc. They promise to provide better service in the future. We should have been allowed to take the rental gear with us when we checked out, and it was improper for the 2nd associate to demand additional payment for that privilege, and to interject into the conversation at all. They've offered my buddies rental gear on the next trip - not an insignificant amount of value.
I received a heartfelt (I feel) apology from the owner and the manager for the short fills, and Nitrox misunderstanding. I told him I would be back later in the summer to give them another chance.