As someone who went paleo to heal folliculitis, and did, I can tell you it's probably not the ghee. Are you using some kind of soap or lotion? Have you taken antibiotics, any other medications recently?
My chronic folliculitis ended up being a combo of that and seb. dermatitis. Topicals would clog the pores causing the folliculitis reaction. Paleo helped alot, but it didn't go away 100% until I stopped using any and all topicals. I struggled with this for 3-4 years on my face.
What is your environment like? Humid? Are you sweating alot and wearing tight clothing? Since your diet is so dialed in, I would guess that this is another factor, as mine was.
As grenadine said, it's possible you came in contact with staph too.
Do you have hypothyroidism or any other auto immune issue? This also can explain alot. If you are hypo you might need more vitamin A or some iodine. WHen I had VLC induced hypothyroidism, Iodoral and lots of natural Vitamin A helped. Still taking the Iodoral. Too much fat can be inflammatory for hypothyroid patients (read: can be, but not always). This can be something to think about with increased fat consumption.
I would also like to add that raw milk actually really helped my folliculitis...