I got the following error in the 05.00.00.log file when upgrading a multi-portal site (about 15 portals) from 04.08.04 to 05.00.01.

Error: Violation of UNIQUE KEY constraint 'IX_DesktopModulePermission'. Cannot insert duplicate key in object 'dbo.DesktopModulePermission'.
The statement has been terminated.

As a result, most of the portals (haven't checked them all yet) are missing the majority of the desktop modules and other extensions.

I am open to suggestions about how to solve this.  Obviously the duplicate key prevented the necessary records from getting added to the table during the upgrade.

Thanks,
Intura

for future reference:

this happenes when you have portals with no pages, just log in as administrator in the web interface, and delete all portals with -1 pages.
took me a while to figure it out.