Found the problem...
Its twofold; some modded civs have their files completely copied from existing civs, of which not everything is edited correctly. This causes the modded civ to become a 'placeholder' of a default civ.
Example; the Ayyyubids seems to be a copy of Egypt. When you activate it in the mod selection screen, you load the mods, and you go on to the next advanced screen to create your game, either Egypt or the Ayyubids wont appear.
Second problem is even worse and seems difficult to pinpoint. This is that mods need to be activated in a certain order. I first used the trial and error principle activating the civs, that is, activate, check if it appears in the advanced create game screen, if it does, on to the next one, if it doesnt, deactivate mod and turf the civs that dont work.
Strange thing is, some civs didnt activate while I remember I have played them earlier without any trouble.
So I will use this principle from now on; dont activate alternative leaders for the same civs (no 2 Russias, no 2 Englands etc), just keep the default civs for what they are. From there on, activate any civ you like, but keep the trial and error principle in mind. If one doesnt appear or all default civs disappear, simly dont activate it.
Furtheron; the more mods you DONT activate, the better. Keep the game as true to its original as possible.
Now I play on Gedemons Giant World Map (YnAEMP) with 62 civs (edited dll various mod components file, and YnAEMP leader fix) carefully selected as not to let it crash.
I limited the game enhancement mods that dont change too much of the game, and
only what I find are the most important, like more religions, more beliefs, submarines ignore borders, captured settlers remain settlers, lumber mill on jungles, chopping jungles give production, policy plus, embark units with sailing, lighthouse on seas and lakes, friendly waters, delete stupid sci-fi units, stronger cruise missiles, lancers to cavalry, pikemen to musketmen, bowmen to cannon, feudal ranks, faster aircraft, quick turns, trading posts grow into towns, one wonder per city per era, and some wonders.
Now it works like a charm.
