Sounds like your problem is ethical. To be honest about it, or not. I'm not sure I can really answer that for you!!
When it comes to telling future partners, it's always best to be honest. But personally, I don't understand why the military even has the right to be asking those question. After all, they can forbid someone from being in the military for being gay, can they?? (I don't really know, but that would go against human rights...) Do they actually say that you CAN'T join up if you are positive for herpes. That's just wrong. As well, if they said people can't join up if they have herpes, 80% of the American military would be kicked out of service!!
Other posts here indicate that the military doesn't actually test for herpes in their STD screenings. So if I understand correctly, the military Dr. said you didn't have herpes but you had jock itch instead?? Is that right?? I'm assuming that you have been tested for herpes before and you KNOW it's herpes??
Either way - if you've told the Dr., and he didn't do anything - you've been truthful, right??
At this point, it really is personal ethics...