Force IE 11 compatibility mode for certain sites within domain

You can do 1 of 2 things I believe:

The GPO policies are located in:

Windows Components\Internet Explorer\Compatibility View

(both user and computer settings have them depending on how you want to deploy them)

You can either turn off compatibility mode completely for the browser: "Turn off compatibility mode"

Or you can disable compatibility mode just for intranet sites: "Turn on Internet Explorer Standards Mode for Local Intranet"

See here: http://support.microsoft.com/kb/956197

Turn on Internet Explorer Standards Mode for Local Intranet: This setting disables Compatibility View (enables Standards Mode) for all intranet Web sites.

I've never had occasion to have Group Policy Administrative Templates "partially apply" in the manner you're describing. My gut says that the root cause is that the specific GPO that sets the "MSCompatibilityMode" is either not applying to these 100 users.

Is the "MSCompatibilityMode" setting (called "Include updated Web site lists from Microsoft" in the Group Policy management console) being set for the users in the same GPO that contains your other IE8-related settings (the ones that you're talking about when you say "though they did get other IE8 policies")?

I'd run the Resultant Set of Policy (RSoP) MMC snap-in on an a user who is getting the right settings and a user who is not and compare the lists of GPOs applied.