Sounds like you have TMJ. I've noticed that when my crohn's is bad, the TMJ is bad too. Now that my crohn's is under control, my jaw no longer hurts or pops. It must have to do with inflammation or something.
34 years old, Crohn's disease for 15 of them
Resection of ileocecal valve on 09/22/09
Current Meds: LDN, Pentasa, Effexor XR, Zyrtec
Supplements: 3 kinds of Fish Oil, Multi-Vitamin, Vitamin D, Calcium, Magnesium, Coconut Oil, Garlic Oil, CoQ10, Enzymes
SCD since 12/01/08 - eating Stage 3 foods