I'm having the same issue with my Windows updates. I deploy critical updates to servers once a year and my server 2008 R2 device collection was last updated August 2014. New deployment (all critical updates) was done last week and some of my servers are showing compliant even though I can't see any updates since August 2014.
Tried below and when I run the x64 msu it says "the update is not applicable to your computer"
http://blogs.technet.com/b/configurationmgr/archive/2015/04/15/support-tip-configmgr-2012-update-scan-fails-and-causes-incorrect-compliance-status.aspx
