Hi!
I have this, too. The MRI didn't show anything, but I gather that that is often the case. I have also had scans to rule out any gynae problems as it was much worse at different times of the month. I am now waiting to see a physio to check that my (self)diagnosis is right and to find out whether I should be doing exercises to mobilise that area or to protect it. I have started going to a yoga class, but I am still working what exercises help and what just puts me in pain for the rest of the day.
I have found some useful exercises for SI joint pain on youtube. One that particularly helps me is simply lying on my back (floor or bed/sofa) with knees bent up, then tipping my pelvis upwards as far as possible and clenching buttock muscles (keep lower ribs/waist on the floor). I hold this position for about ten seconds then relax, and repeat it a couple of times. It's only temporary relief, but I also find that if I do it when I get into bed at night I have a much more comfortable nights sleep. I'm not sure if it just puts the two sides of the SI joint back into the right position.
I'm now also having problems with tendonitis which has stopped me using my left arm normally and I am wondering if that explains the pain in my knees as I don't think that is 'bony' pain. I don't know whether it's the Crohn's causing this or the drugs - caught between a rock and a hard place!!
Remember, if the scan shows nothing, it doesn't mean you don't have it. From what I've read, the only way to definitely diagnose SI joint dysfunction is to inject anaesthetic into the joint and if the pain goes away then that's where the problem is.
Good luck!