Welcome to the STD forum.
Your diagnosis of NGU seems accurate. Probably you acquired it by vaginal sex with your partner, although some cases are acquired by oral sex. In most cases, the exact cause of the NGU isn't known; there are no tests for most of the bacteria that cause it. Yeast rarely causes NGU; I doubt that's the problem. And certainly you are not "allergic to her menstrual cycle".
But that does not mean your girlfriend is not infected. Probably she is, even though her tests are normal. CDC and other experts have standard recommendations for treatment of the partners of men with NGU; she should have either a single dose of azithromycin (1.0 g) or 7 days treatment with doxycycline. I'll bet her doctor knows this; most likely the doc didn't understand that you had been diagnosed with NGU. (Since your NGU apparently didn't clear up entirely on azithromycin but seems to be improved on minocycline -- which is very similar to doxycycline -- my choice would be for her to receive doxycycline.).
About your treatment: the dose of minocycline you are taking really is too low to be reliable against NGU. You should speak with your doctor, or the STD clinic, and either take doxycycline for a week (100 mg twice daily), or perhaps increase the minocycline dose for a week, then return to the acne dose.
Also, some cases of NGU that persist after standard treatment are due to trichomonas, which can be difficult to identify accurately in either men or women. Since your NGU may be persisting with continued "irritation", it might be that you both should receive anti-trich treatment. It's pretty simple, just a single dose of metronidazole (Flagyl) or tinidazole (Tindamax).
Please speak again with your partner; you could print out this thread and she could take it to her doctor's office as a starting point for discussion. Alternatively, the best choice might be for both of you to return to the STD clinic and explain the situation there. Most likely they will agree with me and will treat you both with doxycycline and perhaps metronidazole or tinidazole.
Please return with a follow-up comment and let me know how it all turns out.
Regards-- HHH, MD
Dr. HHH,
Thank you for answering my questions thoroughly. Due to the limit of space I couldn't write down all my questions, but you have answered them all for the most part. My partner and I were very pleased with the information you have provided us in regards to our circumstances with non Chlamydia NGU.
I went to my doctor yesterday and he prescribed the doxycycline. My partner and I will practice abstinence until we see how the treatment works out for me and her. If it works out well she will be treated next. Thank you.
Got one final question for you before I let you go. Back in the summer of 2009 when I first had sex with my current girlfriend we used a condom and the next day I used soup vigorously in my groin area in the morning. A few days later my inner thigh started to sweat really bad and burn. It was a hot summer I might add. Later my inner thigh and groin got a little better but I still was having problems.
I went to the clinic a few months later. All my test were negative including Herpes. They said that it looked like yeast in my inner thigh. I later went to the dermatologist and he said it looked like a form of joke itch and he prescribed Xolegel 2% Gel 45GM. It got better but my partner gets really wet , and I sweat a lot when we had sex. The irritation in my thigh would go away and would come back after sex with condoms it seemed like. The Xolegel cream would clear it up then it would come back after sex then it would go away.
This went on for about a year until the first menstrual cycle incident when I went to the clinic and to my doctors office. The jock itch has been gone since my doctor prescribed Lotrison as a PRN back during the first menstrual period problem in 2010. Probably just needed a stronger cream for the jock it but some times after sex it seems like I get a little itchy in my groin. Maybe its just in my head, but can vaginal fluids cause jock itch or groin irritation? You don't think this is related to do the NGU do you? Thanks.