You use old unofficial loader, which can load only .ccb (plist) files from CocosBuilder 1.1.
For loading new version from CocosBuilder 2.x you must use cococs2dx 2.0 (gles 2.0 branch) with official extension CCBReader, which read published .ccbi (binary) files.
But I have problems with version as well.
Its look like, that cocos2dx (cocos2d-2.0-rc2-x-2.0.1) support version 2, but CocosBuilder (2.0RC) publish to version 3.
Do you have changed CCBReader for ccbi version 3?
Thanks for sharing or help with resolving problem.