There are several things in /usr/lib that must not be prelinked (like wine or valgrind). However, there is no way to stop prelink from recursing into these directories (obviously excluding /usr/lib completly is no option) Reproducible: Always Steps to Reproduce: 1. 2. 3.
There seems to be a block line in prelink.conf which works, -b. Added a env.d file to the latest prelink ebuild which would work as soon as a patch is merged to portage ( the bug this depends on )
see recent portage and prelink