It is difficult to recreate the actual case, as it only happens with
the big source tree we have here ('good case! you might say).
    

This sounds familiar. I had the same problems until Jurko fixed a 
seemingly unrelated issuse with
 http://svn.boost.org/trac/boost/changeset/44195

See http://lists.boost.org/boost-build/2008/04/18737.php for the 
discussion.
  

Please try the current bjam from trunk.

I have reactivated <install-dependencies> and everything works...
  

Yours,

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