A strange sequence of events...

As the French, me and the fat old Pope (or several of 'em) had a funny little chain of events:

Turn x: I take Genoa.
Turn x+1: Crusade, the Pope demands that my king personally lead an attack on constantinople.
Turn x+2: After making a sufficient amount of troops, I decide this will be the turn I join the crusade. However, the Pope excommunicates me. Then, guess what, the same turn, the Pope dies! Vote in new Pope! New pope reconciles me. Then, a few seconds later, excommunicates me again!

How???

Well you said you took Genoa, maybe the Pope really like the factions you just opend a can of whupass on. Especially if the pope originated from that land.
Then again he may just be Johnny English in disguise and trying to enforce his notion of the only ting France should be allowed to host is an invasion:)

After being forgiven, your status with the pope is still very low. So if you were at war with any other christian nations or had a unit in the pope's land, that may have been enough for you to be excommunicated again. If not, I have no idea.