It is definitely possible that a single biopsy might miss it because it totally depends on the sample the doc chose to assess. It is also possible to have bacterial folliculitis and fungal folliculitis occurring on you at the same time. I had all of these happen to me. The doc did a first biopsy (single sample) and found bacteria that he believed was a result of occluded sweat glands. I was put on oral doxycycline, clindamyacin lotion, sodium sulfacetamide lotion (all antibacterials). These did not work and seemed to make things worse. Probably because bacteria were killed off and allowed fungas to flourish more. A few months later we did a second biopsy (two samples) and they showed pityrosporum yeast. Over the last 8 months I completed two courses of oral fluconazole, one course of oral itraconazole, and washed entire torso daily with ketoconazole shampoo (all antifungals). These actions got me about 90-95% clear. The small amount of remaining issue (possibly bacterial) has just been eliminated in the past couple weeks with a cleanser called Hibiclen. You might want investigate and try this cleanser, it is good. Bottom line, you are definitely not crazy asking for a second biopsy. Hope you get your issue sorted out.
How about wash with the H&S one or twice per week as preventative maintenance to keep the fungis at bay? That's the simplest thing that comes to mind. Everything else I can think of requires a prescription.