Although, people with hypermobility syndrome have higher incidence of dislocation and sprains of certain joints, like hip joints, leading to pain in that area, it isn't the reason for your pains.
It is more obvious that these pains are due to fibromyalgia.
It is well known that fibromyalgia holds the potential to interfere with sex in many ways.
Muscle aches you have daily have been increased by pressure during intimacy.
Hot shower that increases muscle blood flow and eases the stiffness and pain, is recommended before and after sexual intercourse.
Another useful tip, is finding the most comfortable position and placing a pillow between knees during it.
Pain due to a menstrual period is adding to this painful situation, too.

Best wishes!

thanks that has explained a lot and is very useful!

You are welcome!
Best wishes!
Marija