I've posted a similar question about this, but wasn't aware at the time that the update was what was causing my applications to disappear from the right hand panel. Only "Other" shows. I've done just about everything that I've seen in the forums, such as running ExtendScript Toolkit and checking the paths under "Targets" are correct for each application in CC. I've also gone as far as uninstalling everything, running Adobe Cleaner, and reinstalling everything. It worked, and applications were showing up.. until the upgrade of Extension Manager to 7.3.2.39. Right now I'm using an older version of Extension Manager, just so I can use and download plugins that I need. I'm running Mac OS X 10.7.5 currently. Its annoying to have to see that I have an update available in my Toolbar constantly, so I'd like to fix this. I can give you any info you need.
Thanks.