I am running IIS 7.5 on Windows Server 2008 R2 x64. I added a new app pool via the iis manager and wanted to set the autostart and startmode options in the applicationHost.config file. However, the new app pool is not appearing in either of the applicationHost config files (%WINDIR%\System32\inetsrv\Config and %WINDIR%\SysWOW64\inetsrv\config). The app pool has an application added to it (the application is still listed under the old app pool in the config files, though it is correct in the iis management snap-in). I have run iisreset several times and completely restarted the server.
Does anyone know if these config files are cached somewhere else that may not be refreshing or anything else that may cause this behavior?