That list of updates is present only when the softwareupdate client has previously detected updates. I'm fairly sure that's the plist that causes the number to show up on the App Store dock icon.
Sounds like the plist hasn't been cleaned out properly. See if there are any truly available updates by going to command line, sudo'ing to root and running this command.
softwareupdate -lv
If you have updates available, it'll report them otherwise it'll give you another message.
You can clear the key out by using the following command:
defaults delete /Library/Preferences/com.apple.SoftwareUpdate
and then putting the key name which I can't remember at the moment.
I literally was doing all this, this morning while testing our new reposado solution.
Next time you launch the App Store to do a Software Update and it comes back empty, try doing a refresh (?+R).
I ran sudo softwareupdate --install --all that seemed to work.
App Store.. meh.
I see this fairly often, where the Mac will give me a notification that there are updates available but clicking the link for more details launches the App Store which says there are no updates available. The softwareupdate command will be correct, though.
I ran into this same problem and worked on it with JAMF for about 2 weeks. For whatever reason, the App Store Updates and softwareupdate through the command line don't always agree. Command line will always show the correct updates and the App Store will usually follow suit within a few days time. We had no success using defaults write to point to our SUS and had to resort to using Configuration Profiles, which ultimately worked just fine.
@makander, naturally we don't leave it up to a user running the app store app or clicking "Software Update" on the ? menu, but if for some reason you're trying to update and you're already there... the refresh trick helps.