Maybe this error has the same cause as this case: SQLite error on create new project. Can you try the solutions described there?
By default, Windows Vista blocks write access to the %ProgramFiles% folder for default users. The Modeler needs write access to the folder where the Modeler is installed to create new projects, so you can only create new projects when you have administrator rights.
Disabling UAC may help, but for this case it is better to give yourself write access to the folder where the Modeler is installed.
Yes, it has the same cause. I installed the modeler using administrator privileges (as requested by UAC) into C:\Program Files but normally my account does not have access there. I didn't know that the modeler also needed write permission to System.mpr. For now I will just always run the modeler as an administrator.