I've noticed on several upgrades from 5.6.3 to 6.0, that custom modules will no longer appear in the module drop down list in the Control Panel.

I have traced the problem to the new "Module Category" feature.

The Module Category is actually a Taxonomy tag found in the Taxonomy_Terms table.  This table links to the ContentItems table through the ContentItems_Tags table.  The ContentItems table links to DesktopModule table.   There is a new column in the DesktopModules table called "ContentId".  However , for existing modules, after upgrading to 6.0, this is set to "-1", which thus breaks the whole Module Category paradigm.

To fix manually:

1. Add a record to the ContentItems table.  Use DesktopModules.ModuleName for ContentItems.Content.  ContentTypeID should be "3"
2. Copy the ID of the new record and paste it into the DesktopModules.ContentItemID field for the module you are fixing.
3. Add a record to the ContentItems_Tags table.  ContentItemID should be equal to the ID of the new record you just created in ContentItems.  TermsID is the mapping to the ModuleCategory types.  On a default installation 1=None, 2=Admin, 3=Common.

Reported in Gemini: http://support.dotnetnuke.com/issue/ViewIssue.aspx?id=17548&PROJID=2