Just to remember this:
If you suspect an IIS configuration issue between two core servers, on way to quickly identify differences is to export the IIS configuration to a set of files and compare those files using a file comparison tools.
The solution can also be used on Windows Server 2012.
A. export/backup IIS configuration for IIS 7.5
To export configuration to files on IIS 7.5, you need to use the appcmd.exe tools that is located in the C:\Windows\System32\inetsrv folder.
To create a backup, run the following command:
appcmd.exe add backup <BACKUPNAME>
<BACKUPNAME> is the name you want to give to your backup folder.
The files will be stored in the folder C:\Windows\System32\inetsrv\backup\<BACKUPNAME>\
Another method is this – but I did not look more into it:
B.compare configuration files
I use KDiff3 to compare files.