Prescan has encountered sites or lists that were not updated...

I've been in the midst of trying to upgrade my Project Server 2003 instance to 2007. I encountered an error as below when trying to upgrade WSS2.0 (where all the Project Workspace is kept) to WSS3.0:

Prescan has encountered sites or lists that were not updated because they cannot be accessed using the SharePoint Products and Technologies object model. The most likely reasons for Prescan to skip a list are covered in the Knowledge Base article at: http://go.microsoft.com/fwlink/?linkid=69958&clcid=0x409.

I searched high and low, tried everything as suggested in the Knowledge Base article above. Which I then referred to another Knowledge Base article 923904. I did method 1, it returned no orphaned items and I made sure that root has explicit inclusion on the WSS 2.0 site.

So what do you need to do to get prescan.exe to finish SUCCESSFULLY?

1. Get in touch with your local Microsoft Support and obtain fix KB918743. This is not downloadable, Microsoft will send you an email pointing you to a link that last 7 days.
2. Run database repair for WSS:
   
   stsadm.exe -o databaserepair -url http://server/BadSite -databasename ContentDBname -deletecorruption
   
   
3. Detach the Content DB.
4. Run iisreset.
5. Reattach the Content DB.
6. If PreScan still fails than drop and renew a config database. How to recreate the configuration database in Sharepoint 2003.

The reason for all this as explained to me by Ada Pan (Microsoft Online Partner Support) that this problem also may be caused by inconsistence of SharePoint databases (Config- and Content-Database). Prescan is checking Sites, which are listed in the config database This process runs without issues. Later Prescan checks the sites which are defined in the content database(s). Prescan is trying to access these sites via SharePoint Object Model. This step fails, because the site is not in the config database.