Bacterial infections are tricky. Some are less serious, can sometimes be overcome by a fish's natural immune system (gram positive); some are deadly, require antibiotics (gram negative). Typically, the latter is found in newly acquired fish while the former happens to established fish. Also, bacterial infections are often "secondary" to a preexisting parasitic infection. For example, it's not usually ich which kills a fish but the infection which often accompanies it. Immune system can't handle fighting off both simultaneously.
Typically, one cloudy eye denotes an injury of some sort - two cloudy eyes equals infection. As you are observing, it can go back & forth from cloudy to clear as the immune system tries to handle it. The danger is if you wait too long to give the immune system a boost by administering antibiotics, the fish can lose the eye/go blind. If a fish loses both eyes, that's basically a death sentence.
