Due a flaw in the ebuild some files (especially the shared object files) are installed to /usr/usr.
Created attachment 144887 [details, diff] Patch for vtk-5.0.3.ebuild this trivial patch should fix the issue.
Hi Matthias, Thanks much for the heads up and the patch. I guess my fix for a multilib problem on amd64 made things even worse :( In any case, I just fixed this in portage cvs. Sorry for the inconvenience. cheers, Markus