Hi Miss Emma, I'm sorry you're not feeling well.
I have crohn's and have experienced joint pain as well. Usually in my low back and in my left thumb. Recently I had a large joint effusion of my left knee--very painful and I was unable to bear weight on it for about a week. Always for me, joint pain has been a precursor to a severe flare.
If you are not having a crohn's flare right now, it could be an indication of increased inflammation markers within your body that could be signaling disease. You had a flare 6mos ago that maybe is not completely resolved. I wish your doctor had done some blood work for you that could look for increased inflammation. Maybe a c-reactive protien.
Something else that I'm concerned about for you...you are having some severe symptoms. It doesn't sound like your GI dr is neccessarily taking you seriously enough. Perhaps you could have a second opinion or ask him/her to review your labs and medications to see if you could possibly try something else that could control your symptoms better.
Crohn's is a GI disease and so we see GI doctors. Here's the rub with that sometimes: Crohn's can/does affect other areas of our bodies and often our GI doctors think that if it's not a part of the GI tract, it doesn't concern them. I can somewhat see where they're coming from...but it can also be frustrating for us, because if our crohn's was better controlled, we wouldn't be having these ancillary symptoms. If you can not get an appropriate response from your GI doctor, I would first recommend getting a new one...and then perhaps also consulting with an orthopedist may be helpful. You deserve a physician that will hear you when you say that you have debilitating pain and care about getting you the help you need.
I hope you feel better soon!