Load-Balanced IIS 7.5 Web Server ASP.NET Session State problem

Solution 1:

Judging by your question it seems that you have a central session state server (DB?) that keeps track of the session data?

You must also synchronize the machine key which is used for encryption for any forms authentication etc to work. This might also affect the session identification, I'm not sure.

Configuring Machine Keys in IIS 7

Furthermore, you should make use of the shared configuration between the machines, it might itself fix the issue with different machine keys.

IIS Configuration Synchronization for Web Server Farm?

EDIT: When you changed the site ID, did you try to restart IIS manager to see if the webroot had changed? Maybe the configuration is connected to the ID meaning that a change in ID also modifies stuff like the document root etc