I agree with you on the first thought that you raised that this has more to do with the Svaddistana than Muladhara. I picked up some emotional patterns from previous incarnations, but can't bring it in relation to his question though.
I will try to best explain what he has told me. He is in a stable relationship with the same person now for I think about 12-13 years. As far as I now it is monogamous. He has recently developed an enlarged prostrate (he is only 34 years old), which made intercourse for him painful. He had a PSI (prostrate test) done but all was negative. His concern has more to do with the energy of his partner (he is piano player and teacher) which is ejaculated inside him. He feels that it is the seminal fluids (and in his words his partner's energy) inside him which cause the reaction. Problem is I have never met the partner so I can't really tell who or what this guy is. This student is really extremely aware and has a huge Light inside him which shines wide. He also told me that since he started with yoga (apart from one class a week with me, he does twice a week a programme at home, which I asked him to see, perhaps there is an answer in that, he will bring it next week) he experience severe hot flushes during and after intercourse (he explains it is not the normal sexual type), moments of an elevated state of consciousness during intercourse where he "feels out of it", and a sort of tickling feeling which slowly progress from the prostrate area towards the navel. More than his I can't tell you as I don't know him that well. He only started yoga with me at the beginning of this year. He did Astanga yoga with another lady before he came to me for Hatha.
Why he asked this question, his higher reason, I am not sure. He once told me that his previous teacher wasn't very approving of gay people and he mentioned once that she told them in a class that to be gay is due to some terrible karma you have accumulated in a past life. (I question this strongly and I told him I find her comments very un-yogic like).
This is as much as I can share with you, because that is what I know about him. I hope it helps.
I feel I also need to mention that he is physically not small, petite ot efeminate, but on the contrary he is muscular, large and very straight actually. He is excellent at his asanas and his discipline is astounding to me.