I always have this problem, with /usr symlinked to /d/usr. Untarring an archive at the root removes the root symlinks. I already reported that here, and Alan made the same answer, which is perfectly sensible.
?? How this can be? I can prove that it works (or at least, used to work): download the EasyMiNT Aranym image, install basic, standard and dev packages, login prompt. Now you have gcc and everything. Type 'cd /' and then tar xjf <my libraries>.tar.bz2. It works flawlessly. So I don't buy this symlink story, sorry Alan ;)