Thank you very much for the useful information Jon.
These kind of spots are not specific to only a particular clinical condition rather there are a number of important possibilities.
I would not consider this to be a fungal infection because the fungal infection of the genitalia does not cause raised bumps/spots, rather it give rises to a more widespread and generalized rash (and this is the reason why anti-fungals have not worked).
Some of these kind of spots are age related; but they should not itch in general.
Bacterial infection like folliculitis can be a reason.
Angiokeratomas (small vascular lesions) can be another reason, which are usually present with out symptoms, and persist unless treated (removed by laser). They can appear any time with out any specific trigger. This does not spread from one person to another.
Molluscum Contagiosum is another possibility --- a viral infection that spreads from skin to skin contact.
Bowenoid papulosis is another viral infection which give hyper pigmented lesions and most of these resolve spontaneously.
Finally an atypical presentation of herpes (but this is a least likely possibility here).
Since you have been active sexually, its recommended to get your self screened for STD's and at the same time see your doctor for a careful clinical examination discussing the details i have mentioned to get a specific diagnosis and management plan that suits best to your needs.
Once an exact cause is identified, a specific an targeted treatment can be instituted to eradicate this problem.
I would have been worried too if I were at your place, but let me reassure you that this is a treatable condition and carries a good prognosis with appropriate management.
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