I had quite a few servers that were reporting incorrect compliance for Software Updates to our SCCM 2012 server. After doing Software Updates Scan Cycle on the client, the WUAHandler.log would always say successful. When doing a Software Updates Deployment Evaluation Cycle the log UpdatesDeployment.log said:

EnumerateUpdates for action (UpdateActionInstall) – Total actionable updates = 0

So if there were no updates available to be installed, why were my Software Update compliance reports showing the client as non-compliant and the Deployments in the Monitoring node in the console saying the client In Progress for a Software Update group deployment?

This blog post saved me http://blogs.technet.com/b/scotts-it-blog/archive/2015/02/23/refreshing-state-messages-in-system-center-configuration-manager-2012.aspx

This PowerShell script in the blog above forced my client to re-send its compliance to the SCCM 2012 server:

$SCCMUpdatesStore = New-Object -ComObject Microsoft.CCM.UpdatesStore
$SCCMUpdatesStore.RefreshServerComplianceState()

Then when checking UpdatesStore.log on the client:
Successfully raised Resync state message.
Resend status completed successfully.

I then checked the SCCM 2012 console in 15 minutes and the Deployments section in the Monitoring node showed the client as Successful instead of In Progress, and the SCCM 2012 update compliance reports showed the client as Compliant.