Well I, using the IGF build, have no Scenes.ini in Coalition.rte, but that probably doesn't help you.
I would go to <whatever your cortex command path is>\Coalition.rte\Scenes.ini and comment out the offending line. (line 3)
See:
Code:
IncludeFile = Whatever.ini *It was this
// IncludeFile = Whatever.ini *Make it this
See if that works/causes an effect on the game.
Or else you could comment out Scenes.ini itself from Coalition.rte's index.ini
So in <CC path>\Coalition.rte\Index.ini change:
Code:
IncludeFile = Scenes.ini
*To
// IncludeFile = Scenes.ini
Are you using a Mac, by chance?