Is this a problem or I am doing something wrong ?
The doc on the wiki and the README.building in the tree specifically says you need to install libosmocore from the GIT and _NOT_ the one embedded in the tree. The one in the tree is a special version for the ARM code and must NOT be used on the host.
You must not go and muck around with the build system. Just doing make in the src/ dir should be all you need to
Cheers,
Sylvain