And regarding a cyst giving a false positive pregnancy test, yes it is possible, but very rare. Hormone secreting cysts are very complex cysts and are not the "normal" cysts that most people refer to.
It really depends on the type of cyst and the size. I've had normal ovulation cysts, benign teratoma cysts (dermoids), and malignant teratoma cysts. The only ones that I ever felt were my first one (malignant teratoma) that was 9 cm and caused dull constipation-like pain due to its size, and my current cyst is a normal 'functional' cyst at 5 cm. I had pain with this cyst that landed me in the ER, most likely because my ovary was hemorrhaging into the cyst. The pain you feel with a cyst is going to be a sharp pain that doesnt go away no matter what you do (normally indicating torsion if it cuts off the blood supply to the ovary). The only constant pain I've ever had was from the 9 cm cyst, but at that point I looked 4 months pregnant due to its size so there was no denying something was in there. I've had cysts for 8 years and have never had any pain that is similar to menstrual cramps, its a very distinctive type of pain once you get to recognize this. I also only have one ovary and have never missed a period due to a cyst. However, if you have PCOS (a medical condition unrelated to spontaneous cysts) it can cause irregular periods because you don't ovulate every month.
If you are missing multiple periods with negative pregnancy tests, go to the doctor and have a blood test done. If that is still negative and you are presenting with pain, they may choose to do an ultrasound to look at the ovaries (and if you are one of those people that keep getting negative tests, this will confirm or deny the presence of a pregnancy). Most often, people get cysts and have no idea they are even there until they rupture on their own without even knowing.
For example, would a cyst cause you to spot a little at the same time you'd normally have a period for several months in a row? Or would it just make your periods irregular/nonexistent instead?
Should you expect to have pain, and would it be any different from menstrual cramps?