I think that your problem might be that you have more than one modular leader for one civ here. Marpesia and Penthesilea are both Persian leaderheads and Joan of Ark and Delahaye are both France ones. Modular mod work by adding/changing xml file entries instead of replacing whole files like normal mods work. Since the leaderheads have to be assigned to a civilization in their CIV4CivilizationInfos.xml entry, they overwrite the standard entry of that Civ for the game. However, if you load another leaderhead for that Civ, your just replaced entry gets replaced again, and only the newer leaderhead will be assigned correctly.
But luckily only some little changes are necessary to correct this. Just open the CIV4CivilizationInfos.xml files of the two leaders assigned to the same civilization and add the others entry respectively. For example, for Marpesia and Penthesilea you need to open the "Marpesia_CIV4CivilizationInfos.xml" and the "Penthesilea_CIV4CivilizationInfos.xml" in the "Custom Leaders" folder, go down to the "<Leaders>" entry and copy&paste the
into the "Penthesilea_CIV4CivilizationInfos.xml" file and visa versa.Code:<Leader> <LeaderName>LEADER_MARPESIA</LeaderName> <bLeaderAvailability>1</bLeaderAvailability> </Leader>
Now both leaderheads should work. You just have to remember to remove that entry again if you should remove the respective leaderhead again while keeping the other one.
I will certainly give that a shot. It would explain how one shows up in one place and not the other. I was wondering about that when I was copying original Civs and saw a list of leaders instead of just one. I should have left well enough alone.