Windows 8, Java 1.8.0_25 64 bit
When using the command "/kill @e[type=Shulker]", shulkers that have been spawned in using spawn egg are not killed, giving the message "That entity cannot be found". However, shulkers spawned in using the "/summon Shulker" command are killed correctly, and exiting & reloading the world allows egg-spawned shulkers to be killed with the command.
Use a Shulker spawn egg to summon a shulker.
Use "/summon Shulker" to summon another shulker nearby.
Use "/kill @e[type=Shulker]", only the second shulker will be killed.
Close then open the world, re-type "/kill @e[type=Shulker]" and the second shulker can now be killed.