After prelink ran on a cron job, my eagle-4.16_p2 started segfaulting whenever I tried to use the 'move' command. Reinstalling made it work again. I think eagle has some kind of crack protection too, so it is probably a good idea to have it added to the prelink path mask when it is installed, or at least make a note of it in the ebuild messages. Reproducible: Didn't try
It is a binary package, so according to http://www.gentoo.org/doc/en/prelink-howto.xml it should be in PRELINK_PATH_MASK. I'll work on fixing it.
In CVS. Please test and reopen this bug if the issue remains.