Hold on, I just realised you said scenes.ini in Scenes.rte? Shouldn't it be Index.ini? IIRC that's like the must have file for .rte folders, let me check out my installation.
EDIT:
Yeah, my Scenes.rte is empty except for a very humble Index.ini file that goes like
Code:
DataModule
ModuleName = User Scenes
ScanFolderContents = 1
IgnoreMissingItems = 1
If your contents of scenes.ini is the same, try renaming it to Index.ini, if it's not the same,
copy paste this in a new Index.ini file in your folder. If this isn't it then I'm not too sure what could it be.