If you create a document type that inherits from Page, and then do the following two things, it breaks:

1) Select CMS.MenuItem and also the document type that derives from CMS.MenuItem for the content filter, i,e "CMS.MenuItem;CUSTOM.MyDocType"
2) Add to the Where clause "MenuItemGroup != 'footer'

What appears to happen is that the CUSTOM_MyDocType table is not correctly joined, and so the fields that it derives from CMS.MenuItem are not available to use.