Can't install BASH patch: OSX 10.9.5 update installed, but system still says it is 10.9.4
The best thing to do when the system gets confused is to download the latest combo update (or the equivalent combo update) from Apple and then install it from the package:


http://support.apple.com/kb/DL1761


Once that is done, I would reboot and then download the bash patch and re-apply it as well.


http://support.apple.com/kb/DL1769


Only then would I let the App Store have a crack at more updates.