It says in the manual that the Old Man gives preference to targets that already have a significant Catholic population - he likes using crusades to liberate his oppressed flock. Usually old Cardinal Domingo of Spain and the starting Cardinal of Portugal usually set up conversion-camp outside Cordoba until they die, which would explain why Cordoba stays high on the hit list.

If there's a Muslim stronghold region like Jerusalem that you want to take over by crusade then I'd send three or more priests to convert the population to above a third Catholic (I'm not sure the exact proportion, but the higher the better). It'll take a few turns but you should eventually find it back on Popey's hit list. Usually Egypt bags it early, but unless rebel held Jerusalem gets an early crusade the population tends to get turned to a Muslim majority because of all the surrounding Muslim regions (Islam and Orthodox Christianty seem to be twice as contagious as Catholicism so Catholic minortities tend to disappear quickly in the Middle East).