a strand on Chlamydia that was only 2 weeks old?

So, almost a year ago my girlfriend (which I had been with for 10 months at this point) went for her to her gynecologist because I had a rash on my penis, which I had my doctor look at and he said it was just an irritation and to put some Cortizone cream on it and this was in June 2011. When my girlfriend got her results back she tested positive for Chlamydia. Her doctor gave her the pill form, and I just called my doctor's office assuming I had it too and he prescribed Azithromycin, the one you stir up and drink. We both had follow ups to make sure it was gone. I went back took and pee test and came back negative and so did her follow up. But her doctor was telling her it was a strand on Chlamydia that was only 2 weeks old, and that I cheated on her 100%, and was being unfaithful. Which is not true at all. I have NEVER cheated on my girlfriend nor even thought about it and I know she has never cheated on me. The question is how did this come up? I don't understand.