What is the likelihood for crohn's disease to just flare up during the beginning of my period?

Yes: This is very common. With your period, your body experiences a surge of prostaglandins which causes smooth muscle contraction, contracting the uterus, but also the vulnerable intestine of crohn's. This is believed to be one possible cause, but there are probably other triggers of inflammation. You don't want to use nsaids for pain, though, since they can cause GI bleeding.