Although I didn't do IVF, I was on progesterone, and for a few cycles started it right after O. As TRH said, you won't get AF while taking it. I always stopped it right after a negative Beta. I don't know about the cramps, but have heard this from other IVF'ers, so hoping it's a good sign for you! That being said, if it's worriesome or get's worse, I would contact your Dr. just to let him/her know.
Good luck, keeping everything crossed for you!!!
You won't get your period while taking progesterone and you're right-- IVF doesn't make for anything "typical" but cramping can certainly occur. I had what I would call odd cramps after my 5 day transfer. It was uncomfortable at moments but it was not like my monthly AF cramps. I'm nearing 18 weeks now! Hoping your cramps are baby cramps, too. SSBD!