S.,
I have had ovarian cysts for several years and did not have any complications with my pregnancy, but I'm not sure mine were around during those months since they seem to come and go with ovulation.
However, I have a friend, (who is due any day now!), that had many problems with her cysts before she was even pregnant. She has fought them the entire pregnancy and has had quite a bit of pain associated with them, and with a blood clot she developed as well. Her doctor was able to give her some medication that was a stronger than tylenol, which has helped her a lot with the pain.
The past month or so, she has worked from home part-time since her doctor was a little concerned with what was going on. BUT she was not put on full bed rest so that's a positive. She has been doing better since then and is pregnant with a perfectly healthy baby!
I wouldn't stress too much. I think, unfortunately, these just might be more uncomfortable to you than dangerous to the baby.
Good luck to you, and congratulations!