Denied re-entry for something that was waived during original enlistment?

Every branch has different medical standards...it's possible the Navy doesn't accept that allergy for whatever the reason.

Waivers were much more loose in 2007 when the military had a tougher time meeting recruitment goals. They are more strict now, which affects many people. So you're not alone.

I had a Soldier who had been Chaptered for a drug offense several years ago as a junior enlisted Soldier. A few months after he left the Army, he enlisted into a state National Guard unit and got what he understood was a waiver for his Chapter.
After serving in the National Guard for several years (and doing very well, including getting promoted to be a NCO) he then came back into the Active Duty Army.
When he enlisted into the Active Army he thought he had again gotten a waiver for his Chapter.
He tried to remove the earlier Article 15 from his records and on review of his records, officials noticed that he had marked NO on previous drug use on both enlistment documents (because he thought he had a waiver, he did not have to acknowledge his previous use).

Long story short, he went before a GO to determine the final outcome of his service and will probably not be allowed to serve much longer based on the administrative punishment he received.