Hi there -
Sometimes the pill, or other hormone treatments, can "hide" endo. Many women I know, and many women here, have been told they have endo at one point or another, then they go on some form of treatment, then go back in, and the docs can't see it. I know I had 2 laps before I was finally diagnosed with endo. I had been on the pill the whole time, and I think it kept it small enough that the docs missed it. When I went off the pill, the endo grew rampantly. Its my theory, and not proven, but I have no other explanation.
Also, did they call the blood filled cyst an endometrioma? That is typically found in women with endo. I had one 2 years before I was finally diagnosed, and my doc never linked it for me.
I might try a different doctor, and maybe go to a reproductive endocronologist. Even if she isn't trying to conceive at the moment, they are typically much more aware of what causes problems for women. good luck!