Mac App Store shows pending update for update that was done

I do some back-end things for Macs at our company, and usually answer helpdesk questions when they get stumped. Well, this is stumping me.

We have a user who is running El Capitain on his system. He is a developer, so he does do a lot of things to change his machine, so we anticipate some things may not make sense. He installed a recent security update, which I believe is this one: http://support.apple.com/kb/HT201222

His App Store is still showing that the update is pending. He can't hide it, and he can't run it again. I'm trying to see what this might be. He is the only user of the machine. The other accounts on it are two local IT tech accounts, and macports. The machine is bound to Windows AD (with his profile as a mobile profile) and is managed by JSS.

We manage configuration policies through JSS, and they are closely monitored. I don't see anything different about his configurations than anyone else's.

I've gone through what I would think would normally flush this out. First I had him remove the com.apple.SoftwareUpdate.plist from the Library. That didn't do it.

Then the following removals,

rm -r ~/Library/Caches/com.apple.appstore

rm -r ~/Library/Caches/com.apple.storeagent

rm ~/Library/Preferences/com.apple.appstore.plist

rm ~/Library/Preferences/com.apple.storeagent.plist

rm ~/Library/Cookies/com.apple.appstore.plist

Also had him re-index Spotlight, https://support.apple.com/en-us/HT201716 None of these items have remedied the issue.

With a pending Sierra update we'll be pushing out to users, we reckon that might fix it, too. But I'm wondering if there is something here that we've missed.