I think I got it working. There were some paths in the web.config file that had the same problem (\/config). I fixed them, but that caused a major meltdown. That meltdown was due to the LDAPAuthenticationProvider.xml file not copying properly from the patches folder to the security folder. None of the pages would work. I copied that file and ran the sql patches directly on the server and after an IIS restart all was fine again.
Maybe that will help someone in the future.
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