Syphilis - Recent Diagnosis

I have questions about a recent diagnosis I received. I'll try and make it brief.

SInce November '08 I had a number of anonymous, unprotected sex contacts with other men. All involved mutual oral sex.

In January I noticed a lesion on the shaft of my penis at the glans. The lesion was not painful and I treated it with an over-the-counter antibiotic cream for a week. At the same time I scheduled an appointment with the local health department.

About 10 days after noticing the lesion I was examined by a physician's assistant at the health department. The lesion had disappeared by then and the assistant showed me a book where I identified a color picture of lesion which looked very similar to the one I had on my penis. At the same time the assistant found and pointed out a very small, also painless, abscess (for lack of a better word) on my scrotum. THe assistant told me that I had most likely contracted syphilis. I was given 2 shots of penicillin in the buttocks and a swab was taken from my urethra. I was told to return in 30 days for lab results.

Today I was told that all lab results have come back negative and that "all numbers are in the acceptable range". I am awaiting review of these results and will be recontacted by the health department within a week. I have not show any additional symptoms.

Now I am confused. Is it possible that I DO have syphilis and that it was too recent to show in the blood test? Are there other explanations for the lesions on my genitals? How long do I wait before being retested? I now carefully inspect my genitals daily. Absent any more lesions can I assume that I am not contagious? I have chosen to have no sexual contact with others until I resolve this issue but would appreciate feedback from knowledgeable people here while I await recontact from the health department and while I plan how to proceed with my life. Thanks to those of you who reply.