Quote Originally Posted by Von Nanega
Check your diplomacy screen. You might be en enemy of someone the pope is allies with.
I had a weird thing in my first campaign when trying to ally with the Pope, took ages and I didn't have the option. Then when i did and managed to ally, the diplomatic messages came up (i.e. peace between you and another faction or a break of an alliance somewhere) and France who was an ally before I destroyed them came up in a message saying they were at peace with me .... even though I had destroyed them years before.

It happened again as the Danish and the English were destroyed and when getting the HRE as my vassals I was again at peace with a destroyed faction