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When you open a file with SharePoint Designer, it creates all kind of FrontPage Server Extension functionality in your web application. One thing it does it that it creates a _vti_cnf folder in every folder you have in your web application. If you remove all these folders you fix your problem.

I don't know of a handy DOS command to delete all these folders recursively, but with some PowerShell I solved the problem.

Open a PowerShell prompt, set the current directory to the folder hosting your web application and execute the following command to see the "damage":

PS C:\Inetpub\wwwroot\wss\VirtualDirectories\wss3dev> get-childitem -path . -name _vti_cnf -recurse
_vti_cnf
App_Browsers\_vti_cnf
App_GlobalResources\_vti_cnf
aspnet_client\system_web\2_0_50727\CrystalReportWebFormViewer3\CSs\_vti_cnf
aspnet_client\system_web\2_0_50727\CrystalReportWebFormViewer3\html\_vti_cnf
aspnet_client\system_web\2_0_50727\CrystalReportWebFormViewer3\Images\ToolBar\_vti_cnf
aspnet_client\system_web\2_0_50727\CrystalReportWebFormViewer3\Images\Tree\_vti_cnf
aspnet_client\system_web\2_0_50727\CrystalReportWebFormViewer3\JS\_vti_cnf
wpresources\_vti_cnf
_app_bin\_vti_cnf

Now execute the following PowerShell command to kill all these folders and become a happy camper again:

PS C:\Inetpub\wwwroot\wss\VirtualDirectories\wss3dev> get-childitem -path . -name _vti_cnf -recurse | % { remove-item -Path $_ -recurse }