same here . .I just tried to upgrade from 3.11 to 3.22 and now I get the same thing.
I'm checking the files table and comparing them to what is in the filesystem and i'm not seeing files missing that are in the table (I do see extra files but I don't think that is the issue since I've removed some to test).

I know I'm willing to through some reward toward finding this solution.  Can someone maybe write a util to dump a report of what isn't jiving? so we can either add the files back it thinks it's missing or??

Thanks - Jeremy

I haven't had any luck.  I wrote a program to create a list of the files (in the files table) and check to see if they exist.   They all do! So I'm back to the drawing board... paying a dnn consultant to see if he can figure it out.

I wish there was a way to escalate this.  It's definately some bug that needs to be fixed.  I already mentioned I'd reward someone if they can fix it.. anyone $50? 

I had this same problem. I went back and re-applied all the SQL patches from 03.01.01 forward and everything is now working just fine. NOTE! make sure that your replace the {databaseOwner} and {objectQualifier} identifiers in the scripts or they will not work. For me to do this I used notepad and then [ctrl][h] or find and replace for each. I replaced {databaseOwner} with dbo. and {objectQualifier} with MyPortalName_

If you have the default install you should probably just replace {objectQualifier} with nothing but you will need to check to see if you installed with any object qualifier.