Debbie,
For me, I was told I had IBS for years, but when I went off birth control I started having different digestive symptoms and rectal bleeding. They were really concerned about it being Crohn's or something like that (bleeding is NOT a part of IBS), so they did a colonoscopy, and found a "questionable" looking area on my sigmoid colon (the part lowest down), and then a growth where my appendix should have been - they weren't SURE at the time, but they guessed it was all endo because of my history. So then they did a CT scan, found out that my appendix was HUGE, and that the growth did look like an endo cyst (they didn't want to biopsy it during the colonoscopy, since it was already determined I'd be needing surgery for it). But obviously, until they took it out they couldn't know for SURE that it was endo.
Since I also had a cyst, and the big concern for endo, I wound up having a joint surgery between my gyn and a general surgeon specializing in colon surgery. In all, they drained an ovarian cyst (functional, not endo), removed a bunch of endo lesions, detangled a tube that was covered with adhesions, and then took out my appendix, the cyst growing out of that into my colon, a few inches of large intestine, and an inch or so of small intestine (to make sure they got it all), and they biopsied everything. They're still not sure about the sigmoid part, because that's a riskier place to operate and they decided to leave it be - the outside looked normal, but the inside still looks funny. The cyst in the colon WAS endo, and the appendix was all filled with it too.
What tests have you had so far? I didn't have to have a barium enema (thankfully), just the CT scan (with TWO bottles of barium contrast to drink, PLUS IV contrast - ugh). Even if your appendix doesn't hurt at all, it might be worth having it checked out (usually a CT scan) - apparently that's one of the places most likely to get endo, because of it's proximity to the reproductive system. And pre-surgery, another thing they threw out there as a possibility for my issues was chronic appendicitis, where the appendix gets mildly inflamed frequently, which can cause a lot of digestive issues.
Another thing to do is to track your digestive symptoms relative to your cycles (and also in relation to foods/stresses/etc). If you can find a pattern, it gives the doctors more to go off of.
My GI dr said that any adhesions or endo lesions attaching to your colon can REALLY throw your digestion out of whack. So if they can't find any other cause, it might be worth considering a lap, just to make sure.
If you have any more questions about this, let me know! I'm pretty well versed in problems of the digestive system by now.
Good luck!
-Cathy