Eye problems are a very common problem in chameleons, and as you said, most causes are bacterial in origin, but other factors are culprits as well: fungal infections, trauma, foreign body, ulcer, etc. Blindly applying an antibacterial substance without knowing what you are treating is really shooting in the dark, especially if the eye "was bad, then got better, and is now bad again". Most likely the infection has now mutated and is resistant (meaning, its made itself stronger).
Some eye bugs are easy to cure; some are very, very difficult. For example, my big Panther male started unexpectedly shutting his eye after his move to his summer cage. My DVM cultured a nasty bug that was luckily sensitive to an easily administered oral antibiotic. Ten days later, Presto! eye is fine with no recurrence. Another Ambanja I just got in as a rescue has an obviously chronicly irritated eye; it cultured again a nasty bug that unfortunately is resistant to what are considered the safer antibiotics. We are hitting the infection with some pretty strong injectable and topical medications but because the eye has been infected for a good length of time before she received the proper antibiotics, the infection is not responding to treatment and unfortunately, it appears the eye will have to be removed to save the cham's life, to prevent the infection from advancing and rupturing the eye-globe and the infection then entering the bloodstream. What is the point? Eye infections can turn into big problems if they are not treated correctly and quickly. In the above scenario, it is highly possible the latter chameleon could be enjoying perfect eyesight right now instead of on the verge of having her eye removed if the eye infection had not been allowed to linger by adopting the "well, its not getting better, so let's see what I have around the house to treat it" attitude. I have never had a closed eye on a chameleon get better "on its own".
Betadine is an iodine-based product as you probably know, and while it is generally considered safe for use around the eye areas, there are many different percentages of povidine manufactured and some are caustic even to bare skin, let alone a delicate eye. Please do not apply Betadine to your cham's eye without consulting a Dr. He or she may very well advise a povidine-based solution as a flush or treatment, but a vet should be consulted for the specific concentration to be administered. Most of the commonly obtained Betadine scrubs and solutions are designed for skin, not eyes. Please consult a vet first! And have him or her culture the eye(s) & turret(s) to see what exactly is growing in there!
~Kerry I.
Licensed Vet. Tech.