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.