User GPOs Partially Applied

We discovered an issue where some of our GPOs aren't being fully applied to our users and our Help Desk informed me that it's been happening for about a month.  GPResult -r shows that the policy itself is being applied, but the settings within the policy aren't .  Using the Group Policy Results wizard yields the same results and shows no errors.

The issues that we've noticed so far all seem to deal with Internet Explorer where the default homepage, Trusted Sites, and security levels aren't being set properly.  Most of our users are standardized in IE8, but we do have a few running IE10 and the behavior is the same in both versions.  These policies were working just fine and we don't know exactly when they stopped.

Our users are all on Windows 7 and the domain level is 2008 R2.
FAFCUAsked:
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FAFCUConnect With a Mentor Author Commented:
Even though we are seeing this on some IE8 machines as well, this seems to be the cause for the machines that are running IE10: http://www.policypak.com/blog/entry/why-does-internet-explorer-maintenance-go-away-when-ie-10-is-installed-and-what-can-i-do-about-it.html

I'm going to adjust our IE GPOs and see if that fixes both IE8 and IE10 issues.
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Will SzymkowskiSenior Solution ArchitectCommented:
Do you see anything in the event viewer? Do you have any policies applied at a higher level which might be causing the other policies to be filtered out? If you use RSOP.msc and check the settings do the policies show up that should be there?

Will.
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FAFCUAuthor Commented:
Will

I don't see any errors in the event viewer relating to the policies.  Regarding the OU that we first discovered the issue on, the main policy that is an issue is the first link.  Running rsop.msc also shows that the settings are not being applied even though the policy is.

This isn't affecting every user but we haven't found any pattern yet as to who it does and does not affect.
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FAFCUAuthor Commented:
Per the article linked in the accepted solution, Microsoft deprecated the Internet Explorer Maintenance group policies with the release of IE10.
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