I have two identical Mac Minis and I updated each with all available updates. This caused both machines to go from OS X 10.9.2 to OS X 10.9.4.
uname -a reports different kernel versions for each machine:
Darwin oaxaca.local 13.1.0 Darwin Kernel Version 13.1.0: Thu Jan 16 19:40:37 PST 2014; root:xnu-2422.90.20~2/RELEASE_X86_64 x86_64
Darwin morelia 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64
Why does morelia have a higher kernel version (13.3.0) than oaxaca (13.1.0)? On oaxaca when I open App Store and click Updates, I am told that no updates are available, so it's not clear to me how to get oaxaca to show the same kernel version.