there are two different commands to show the config
one has options, the other not
(Cisco Controller) >show running-config ?
(Cisco Controller) >show run-config ?
commands Display list of configured commands on WLC.
startup-commands Display list of configured startup commands on WLC.
no-ap Display running configuration of controller without AP configuration.
<cr> Display running configuration of controller.
I guess your difference is created that in the background "no-ap" is specified
which results in the controller config only , without the ap-configs