Error when trying to create a new menu definition

When I create a new folder and add a new menu using portal site manager, it
results in NullPointerException. It happens only when a new menu is added.
If I add the menu manually by opening the folder.metadata and then adding
another menu using portal site manager, it works fine.

If I have the pages in database, It works fine. Only when the pages are in
file system its results in the error.