My gelding has sort of the same problem, and I think it was a deworming issue. Plus the bugs were so bad this year that he was itchy all over. What I've done is deworm and now I've started apply the M-T-G on the area. The M-T-G should help sooth the itch and help grow the hair back, two birds with one stone .... yay.
However if this wasn't helping my gelding I was going to get a vet out to do a skin scrapping to see what else might have been bothering him.
I had that with my gelding Sammy. I just slathered the hair loss areas with Lanolin Rich ointment from Corona. Stopped his itching (poor horse was scratching his head on everything he could find) and the hair started growing back pronto.
Never did find out what really caused it. I figured he had problems with some bug out in the field.