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 right now). 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?