Buildroot overrides certain directives in kernel configuration. Example: when doing a clean build, unless BR2_TARGET_ROOTFS_INITRAMFS in Buildroot's config file is set, kernel is built without initramfs support despite it was enabled in file referenced by BR2_LINUX_KERNEL_CUSTOM_CONFIG_FILE. On the other hand if BR2_TARGET_ROOTFS_INITRAMFS is set, kernel image contains complete root filesytem. This is unacceptable - this way it is a problem to build kernel with initramfs support but without actual filesystem embedded in the kernel, Buildroot shall not be such invasive when custom configuration file is provided.
This has already been fixed at http://git.buildroot.net/buildroot/commit/?id=ee3f319249e146d92b093ad8c45a3a908d44236f The fix will be part of the upcoming 2010.11 release.