Just an update, I called the vet and told them what is going on. They suggested these options:
-bring him in today to get him re-examined
-get him some new antibiotics that would be administered twice a day
-get a refill on his old medicine
I forgot to mention the possibility of parasites, but I might call back later with more questions.
Also, I would like to bring in a fecal example just in case it is any different from a cloacal wash.
Right now, he's just resting in his little cave.