In order to make the common case as fast as possible, the x-kernel build procedure normally doesn't check to see if any source code in the system areas needs to be recompiled. If you make a change to any of the system areas, that code will have to be recompiled explicitly from the build area using the targets for that area. For example, if you add a protocol to the system protocol area, in addition to modifying the protocol Makefile you should run these targets:
make protDepend
make protCompose
make prot