My experience, both personally and in research is that cysts are a common side effect of Clomid. It is very important that you have an u/s done at the beginning of each cycle to rule them out. They will not put you on another dose until the cysts are gone because Clomid tends to make them larger. They usually go away on their own before the next cycle. I have always been told to drink lots of water to help get rid of them. Not sure if it really helps or not.
My understand of a cyst is that it is either a left over follicle that did not release the egg or the left over corpus luteum. It seems to me that they simply change names at different time of the cycle!
Good luck. And here's hoping that this is your last month on Clomid!! (sorry about the headaches!)
Love,
Rhonda