Backed up and deleted /etc/asterisk. Upgraded from 1.4.xx to 1.6.1.1-r1. After the upgrade, the most of the files in /etc/asterisk were owned by root:root. Extensions.conf wasn't loading properly (and there was no errors/warnings/debug messages saying it was the problem). Changing the group of all files in /etc/asterisk to asterisk fixed things. Reproducible: Always
This could only be done with a recursive chown in the ebuild which could overwrite the custom permissions that others have. There isn't even a 1.4 ebuild in the tree, so the upgrade path that you're following is not supported in the first place.