the antibiotics killed off the 'bad' bacteria, but also killed 'good' bacteria and other organisms. Competition between these organisms inside us helps keep any single type from running wild and over multiplying. Sooo, when you take antibiotics, it's not unusual for this kind of thing to happen.
Once you're off the antibiotics, a normal flora of critters will re-establish and ballance will be restored. Try the acidophilus - can't hurt, may help. No, you don't have to keep using it forever. Just til you get a good diverse population of organisms back.
(ain't biology fun!?)