The init script expects this directory to exist, but it doesn't create it if it's missing, which is the case after a reboot.
I can also confirm this is the case. I can also confirm that manually creating /var/run/anope first doesn't help create the pid file. My hunch is that anope daemonizes on execution and makes the init script think it terminated.
Could I get you to try with the init script here, and see if it is still a problem? http://dev.gentoo.org/~gurligebis/files/anope/anope-init.d
Bjarke: That script worked.
You know I think that bopm should do somethign similiar in its initscript. it also seems to suffer from pid file barfage
Also fix the copyright date. This is 2013
Fixed, 1.8.7-r1 has the new init script.