I had a similar problem with trying to update using the App Store, and being told that the software was "installed" yet I was still only running 10.8.3.
The App Store was continually saying the 10.8.4 was available but with many tries I still could not download or install it.
And there are a few links to the OSX 10.8.4 (Combo) update that actually lead to a "Cant find this page error" on the Apple site and the App Store.
I did find a link to just the vanilla flavoured OSX 10.8.4 update here at http://support.apple.com/kb/DL1658 which is a smaller download of 359mb rather than 849mb with the combo update.
The simple OSX 10.8.4 update downloaded fine with Safari and I installed it with no problems from the finder. A few opening's on closing's of the App Store app made the update flag finally disappear.
I have since come back here to report this and then found the link to 10.8.4 Mountain Lion Update v10.8.4 (Combo) at http://support.apple.com/kb/DL1659 above and found that this link also starts to download the update through Safari and while I decided that I no longer needed it, I would presume that it would still install fine from the finder like the OSX 10.8.4 update did if you want to go that way.
So it seems to me that there is a problem with (maybe occasionally) updating from the App Store, but if you download from either of the two "hard" links above and install from the finder it should be fine.