Busybox build must depend on busybox configuration file date. If you change busybox configuration file and remake buildroot, it won't rebuild busybox. So you need to manually delete output/build/busybox* dir to make it recompiled.
In order to change the Busybox configuration, one is supposed to run make busybox-menuconfig, make busybox-xconfig or make busybox-gconfig. Those targets take care of removing the appropriate stamp files to force Buildroot to restart the Busybox build process at the next 'make' invocation. If you are modifying the Busybox configuration file manually (without going through these 'make busybox-*config' targets), then I would say you know what you are doing and you know you need to take some action to make Buildroot restart the build of Busybox, for example by running 'make busybox-rebuild'. If we do that for the Busybox configuration, what shouldn't we do that for all the source files of all packages? I.e, I modify output/build/linux-3.0/init/main.c, and at the next 'make' invocation, I want Buildroot to figure out that the kernel needs to be rebuilt. It is unfortunately not possible to achieve that without re-doing a make invocation in all packages, which is not really reasonable.