CF11 on Windows 2012 Multiple Domains Issue - will load directory, but not direct CFMs

Just to clarify, when you select "All" sites, it sets some things globally for all (present and future) IIS sites, but some things only for existing sites.  The handlers (cfc/cfm/etc. file handlers and similar settings) are added to the global IIS config.  The "jakarta" subdirectory is only set on existing sites.  So if you add additional sites later, you need to run the WSCONFIG process twice - once, to remove "All" sites; then again to reinstall to "All" sites so the new sites get setup correctly.

Alternatively, you can use WSCONFIG to connect to each site individually - then if you add new sites, you only have to connect the new ones as needed.

Do you have a "jakarta" virtual directory on the second site? If not (and sometimes using the "all sites" option in WSConfig doesn't do it properly), then create a virtual directory pointing to C:\Coldfusion11\config\wsconfig\{instance id} where {instance id} is the numbered subfolder created by wsconfig for your site(s).