Matt, I've been having the same problem. I got out of balance after taking some antibiotics and I'm having on again, off again problems with my bowels that aren't the result of anything I've eaten, anything going on in my life, or from my usual excess bile problem. I'll get better after a few days, go off the yogurt and acidophillus, only to get messed up again.
Yogurt has both calcium and probiotics in it, both of which can do you some good. So long as it seems to be helping, just keep taking it until you get so sick of yogurt you can't stand to think about eating another carton of it. Then see if you can function normally without it.
If you want to boost your probiotic intake, you can get some at a pharmacy or grocery store pharmacy. You can get plain acidophillus pills in the herbal section, or you can get more expensive probiotic mixes like Digestive Advantage or Culturelle (you may can only find them in a phramacy, not at the grocery store). You can find them in with the other intestinal medicines (like with the Imodium and fiber drinks). Probiotic pills have a lot more good bacteria than yogurt, but, like fiber, they can make you gassy while you're adjusting to them. I haven't adjusted at all to the Culturelle, although I am better with the plain acidophillus now. I take a pill at night so that I can sleep through my gassiness.
I'd take the yogurt and/or probiotics for at least two weeks--not that taking them for a month will hurt you. If you get completely well, good! But don't forget to return to them if you get sick again. Some people are just more supceptible to having gut problems than others, so it never hurts to keep yourself boosted when you get sick, when you have to take antibiotics, or even when some "bug" is going around the dorm or you're in the middle of exams and are stressed out. Our intestines are actually a big part of our immune system; if you keep them in shape, you're less likely to catch stuff or suffer as long. My GI's nurse said she took the Culturelle a week before she went to Mexico, all three weeks she was there, and for a week afterwards; and she was the only person in her group that never got "Montezuma's Revenge". She swore by probiotics to keep you healthy.