((((Belinda)))):
Your description sounds very much like those cysts are endometriomas, cysts caused by endometriosis. They can be very complex, and your CA-125 can be pretty high (mine was 200) but if they are endometriomas, they are benign.
The pain that the doctor is describing to you would be because one of the cysts had ruptured

-- this can be very painful, and can "seed" endomtrial cells, so generally they'll put you on some activity restrictions (for me, it was no lifting and no sex) to protect yourself.
The progestin is an attempt to shrink the abnormal endometrial tissue that is found in endometriosis, and if that second ultrasound shows that the cysts have shrunk, that may well answer the doctor's questions about what is causing them.
Remember that ultrasound can't actually confirm cancer...but given your history, and that the cysts are fluid-filled, it's likely that they're "benign" (although I have a hard time thinking of severe endo -- which I have -- as being totally "benign" given that it forms its own blood supply and causes so much misery).
Has your doctor done a CA-125? It's far from perfect, and in endo can be pretty elevated. But if the unthinkable happens, you'd be able to use the CA-125 to track your progress.
I find that although waiting is the hardest, if I keep busy and active, it at least progresses a little faster -- and I don't have time to obsess quite so much about the "what-if's" (around here, they call that cancerhead). And if those cysts are endometriomas, you may be able to opt for a laparoscopic procedure that also looks at any more endomtrial implants and "cleans" them up.
Take care, and let us know what that followup ultrasound shows, OK?
Audrey