Sorry I couldn't help sooner. I've been having the same problem for the past couple of months and only JUST NOW figured it out!
To be clear, the problem I had was that when I opened App Store > Updates, I got an error dialog: “An error has occurred” “Can't connect to the Apple Software Update server.” Sometimes though, instead of getting this error, the update list would appear, but hitting the Update button just caused a progress bar to flash quickly, followed by a button change to "Installed", only to revert back to "Update" again. Checking the software version confirmed that the update had failed, even though it went through all the motions.
The solution was first to ensure that Time Machine has an up-to-date backup, then to restore from this backup. The reason this works is that restoring from Time Machine restores the file permissions which, at least in my case, was the source of the problem. Note that using Disk Utility to repair permissions DID NOT WORK.
Further investigation revealed that the bad permissions that broke App Store Updates is localized to just one folder named "private". This folder is invisible and located in the root folder (e.g. Macintosh HD). How could permissions go bad on this invisible "private" folder? This can happen by choosing Get Info on the root folder and selecting "Apply to enclosed items...' under Sharing & Permissions. Don't do this! (Yes, I did this, trying to eliminate a bad user name "Fetching..." which had R/W permission everywhere. That was before I realized it had this nasty side effect of breaking App Store Updates!)
If you don't want to wait for a full restore of your entire hard disk, you might first try the following (although I have not tried it, it may work). First, be sure your Time Machine backup is up-to-date. In Finder, choose Go > Go to folder... and enter "/private" (without quotes) in the text box, then hit Go. This opens the invisible "private" folder. With this folder on top, Enter Time Machine with the latest backup, select all, and Restore. This should have reset permissions. Now go back and try App Store > Updates. If that doesn't work, you may need to reboot to do a full Time Machine restore.
After 2 months of bothering the local Genius Bar and a Senior Apple Support Engineer until they stopped speaking to me, I'm finally getting updates! Hope this helps others.