There should not be a "Scenes.ini" file in Coalition.rte unless you made a custom scene and placed it there.
I would suggest opening /Applications/Cortex Command b22.app/Contents/Resources/Coalition.rte/index.ini
Then find the line that says "IncludeFile = Coalition.rte/Scenes.ini" and put two // s in front of it so that it would look like:
Code:
// IncludeFile = Coalition.rte/Scenes.ini
This will make Cortex Command ignore the file completely
Hope that helps