IIS Configuration mystery -- keeps resetting from some default config file?

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I have an IIS installation with three websites. I'm using Zend PHP -- each site is being directed to it's own PHP.ini file. My problem is this -- whenever I go into IIS to make a change, or restart IIS, the server, or mess with any configuration settings at all, IIS is saving my changes to the:

C:\Windows\System32\inetsrv\config\applicationHost.config file.

...but then it's is pulling an earlier configuration and IIS it referencing it as the config. This blows up the sites, tells me each site is trying to use the same configuration and gives an IIS error. I found that this file it's overwriting everything with is in the C:\InetPub\Temp\appPools[somename].tmp

This file is locked -- I can view it in a text editor, but can't make a change to it. It's taking the config in this file, then pushing it to another folder:

C:\InetPub\Temp\appPools[SiteFolder][site].config

I can take the config from applicationHost.config, and shove it into the site.config, and it fixes my problem -- but only until the next change is made...then that file gets overwritten again. I have many other servers with sites set up like this, and any changed made within IIS is written to applicationHost.config and properly referenced by IIS.

In IIS, if I view "CONFIGURATION: SEARCH CONFIGURATION", I pull up the applicationHost.config file and it shows this 'default configuration, and the path shows:

C:\Windows\System32\inetsrv\config\applicationHost.config

But what it shows in IIS doesn't actually match what is actually in that file. If it wouldn't then everything would work. I'm sure this is confusing -- but if anyone can help lead me in the right direction, I'll really appreciate it :)

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