Cysts during before/during fertility treatment and non-ovulation

We've had two very unsuccessful years of trying to conceive. I started getting very painful cysts in 2008 that would make me physically ill when they would rupture. I was seen in the ER for them twice which is how I came to to conclusion that they were ovarian cysts. I got on birth control in November 2008, finished off my 2nd month of it and we conceived our daughter right away in January 2009. My husband and I lost our daughter in April 2010 at 6 months of age to SIDS. After losing our daughter we decided right away to try for another baby.

In December 2011, I was diagnosed with PCOS and put on 500mg/once a day of Metformin. My periods were coming anywhere from 6 weeks to 3 months apart. I happened to start my period the day after I started Metformin which I'm sure was coincidental but my next period came exactly 30 days later but they have not been coming normal since.

In February 2012 I started seeing a GYN about the conception issue. I was prescribed a cycle of Provera to take for 10 days to induce my period in March since I skipped the entire month of February. Forty days later I had my period in April but what is currently happening is that I get a cyst that ruptures before I get my period. Usually the cyst will rupture and then I get my period within 7 days (it never takes longer than that to start). My body has consistently done this cyst cycle for the last couple years although my periods have been very inconsistent that has remained the routine that my body has taken on.

I was also given my first cycle of Clomid (50mg) in March and then when I had the cyst rupture in April I was told to only stay on 50mg of Clomid again. Along with the Clomid I was instructed to do home ovulation testing days 11-18 after my period. I've done that with both cycles and have had all negative tests so far. My GYN ordered a Progesterone lab order which I had done on day 21 and that too was negative for ovulation.

I was instructed to wait for my next period and when that comes I need to call the Dr and they will have me on 100mg of Clomid for the next cycle. However, they said that if I have another cyst that ruptures that I need to call them because the doctor might change the plan if I do have a cyst rupture again. My problem is that when my body gets periods on its own, I never fail to have a cyst rupture. What can cause such painful cysts and is there any other way to stop them besides birth control?