Before working with Mad Level Manager please be aware of this rules. It may help you to avoid difficult to understand issues!
Rule no. 1: Do not use Application.LoadLevel()!
If you were using Application.LoadLevel() anywhere in the project, search for it and replace it with MadLevel.LoadLevelByName().
Mad Level Manager is using its own level loading functions because this is the only way that allows tracking of how player is playing the game. Without it level select screens will not work correctly. Also Mad Level Manager workflow API is much more richer than standard Unity API. Just check it for yourself!
To make sure that you’re not using Application.LoadLevel() anywhere, use MonoDevelop search tool
Rule no. 2: Mad Level Manager does not use scene names
This is because you can build multiple levels using only a single scene with arguments.
Rule no. 3: Synchronize it!
Make sure that all your levels (playable levels, menus, splash scenes) are configured in your level configuration as a level or an extension, and your level configuration is synchronized!