My advice would be to delete the symlink and move any files belonging to Debian packages to /usr/src. Use "dpkg -S usr/src" to find out which files belong to packages. If you don't want to do that, use a bind mount rather than a symlink for /usr/src. Then the /usr/src/linux-kbuild-3.0.0 symlink will work (but /usr/local/src/linux-kbuild-3.0.0 will not).
In other words, the issue remains. Is there a way to ask to the involved package to link via an absolute path rather than a relative one ? May I fill a bug report here ? Thanks, Jerome