I continue this discussion (about pch's) from here: 
http://forums.codeblocks.org/index.php/topic,16866.msg114753.html#msg114753.
As far as I have seen make compiles all sources in one directory,  before changing to the next one.
In our case the first subdirectory (starting from root-Makefile) where we compile anything is 
src/include.
In this folder there are only the pch's to compile. That means they will always come before any source files,unless we change the layout of Makefiles.
Or am I missing something ?