@popcorn - It can take awhile for antibiotics to work and you may have to complete the entire course, or even get more from your doctor before the symptoms of your bowel infection cease.
I would be careful with self-diagnosing as a lot of stomach issues share symptoms. The symptoms of irritable bowel and the symptoms of an infection can be quite similar for example.
If you are really worried you can always get a second opinion from another doctor. Though, I would save my money and just see if the antibiotics work in the time given. Also, there are always over-the-counter medications to help stop diarrhea if you want to try that.