Software Update doesn't show available updates

OS X 10.8.4 (although this started in 10.8.3). When running Software Update GUI (that switches to App Store), it shows no updates, although some are available (e.g. Java when this was posted originally, or Security Update or Airport Utility later). Running

softwareupdate --list

returns

Software Update found the following new or updated software:
       * JavaForOSX-1.0
        Java for OS X 2013-004 (1.0), 65205K [recommended]

and then

sudo softwareupdate --install JavaForOSX-1.0 

installs the update.

I tried cleaning the Software Update cache, it didn't help.

Any ideas what may be going on and how to fix it?

Edit: the same problem with Security Update 2013-03and currently with a new update that is available -- Airport Utility.

Solution 1:

This sometimes helps me when I know that there is an update: Cmd-R. Since the iTunes/iBooks/Mac App Store are all web-based, it forces a refresh.

Your problem sounds more systemic than this, but it’s a quick thing to check (especially for those Java OS X update which hide from me sometimes).

Solution 2:

I had the same problem in a different of OSX and I can say there might be three possible reasons for that.

1.You might have apps installed under different accounts (Yes, you would know, probably not this one)

2.You might have apps installed from different country-appstores and changed back country.

3.You might have apps that are not originally installed from the App Store yet now provided an update from the App Store.

(Actually this answer of mine does not provide a solution but suggests some points to start digging.)