Bad bacteria is hard to get rid of, and often requires a long regimen of antibiotics. But doctors are growing cautious of using too many antibiotics, because of antibiotic-resistent diseases on the rise. At the same time, stopping before everything was gone could mean that what survived in there is now more resistent to anything you're taking--thus why you're not improving as well. It can take even longer to clear them out.
Something you should be doing while on antibiotics, and especially given your situation, is taking probiotics. Probiotics are good bacteria. There's only so much room in your guts for bacteria to live, and if you populate your guts with good bacteria, then the bad bacteria won't have room to spread back out and take over. Culturelle and Digestive Advantage are the two most common and easily-found probiotics on the market; you can find them in any regular drug store in the bowel products section. Personally--if this were me--I'd take a double dose of the Culturelle every day I'm on the probiotics. I think it's stronger than the Digestive Advantage. Probiotics are not harmful, so you can't overdose on them (although you can get gas problems when you first start in on them, the same as when you start a fiber regimen). I read one doctor's article on probiotics some time ago, and he had people on massive amounts of probiotics while they were on antibiotics for any reason, so a double dose of Culturelle won't hurt anything (and, actually, the insert tells you to take two to start with anyways).
I'd take two a day while on the probiotics, and then I'd continue with one a day for at least a month after I get off the antibiotics. Antibiotics kill all bacteria. Probiotics put the good stuff back in. It's kind of like bulldozing a bunch of slums and derelict buildings and then moving in some good citizens who rebuild a nice city.
Also, if you consume any dairy products, get acidophillus milk and eat yogurt. Acidophillus is a type of probiotic. There's not enough in the milk alone to help someone with your serious a case, but it be an added weapon in your fight. It's also something that will help you maintain once you get off the protiotics in the pill form. Yogurt has some other bacteria in it, which can also work as a maintenance drug. I recommend the Greek yogurt, Fage, or Stoneyfield Organic (Stoneyfield is easier to find in your average grocery store). They both have more bacteria in them than the cheaper brands, and they have different strands. The more different strands you have, the better your chances of finding something that gets in there and sticks. Activia is also an option, and should be available everywhere.