Always when i start the game, i get that message. i got the newest patch of Civ4. -The original one, no expansions-
Further it just doesnt do a thing if i try a new normal game, not the scenario. - It plays like no mod is activated-

Some other mods do it to...

You can only play RFC in the RFC Scenario... Normal Games won't work.

I have this exact problem, except it's when I'm playing the RFC scenario.

Yeah, I have this problem as well, does anyway have a fix?

a possible cause to this problem:

you should have the correct Civ entry in your registry.
That is, if you run regedit,
you should have inside

[HKEY_LOCAL_MACHINE\SOFTWARE\Firaxis Games\Sid Meier's Civilization 4]

The key
"INSTALLDIR"="...your civ path..."