WARNING: NOT NOT ATTEMPT ANY CHANGES WITHOUT A COMPLETE BACKUP.
The only thing I can suggest it verify the collation using SQL Server Management Studio. First check the server properties and note the collation method then compare that to the database properties. While it looks like you can change the collation method it is not an easy task.
You might try installing a brand new installation of a DotNetNuke database for testing to see what collation method is used.
I have heard of this problem with SQL Standard Edition before but not with Enterprise Edition and also from upgrading from SQL 2000. Obviously there is something more complicated going on here. Add the complexity of a production server... I'm afraid no one enjoys being stuck in such a bad position.
Here is a script to check your esiting databases:
select name, collation_name, compatibility_level from sys.databases
Enter this in the Host|SQL and click Execute to see the results.
I'm sorry that I don't have a better answer for you.