Unfortunately, while antibiotics can kill off nasty bacteria, they also kill off helpful bacteria, and can cause pretty bad imbalances, so probiotics are often needed to help things go back to where they should be. It can take humans and other mammals months to recover fully from the use of antibiotics, I imagine for reptiles it's far longer. I think it's a good sign that the symptoms have at least lessened some and would hope that the product you ordered will help them return to full health faster.
A virus is always a possibility, but I would assume with the rigorous amount of testing you had done that they would at least have identified there is one present, even if it's not a recognised strain.