The permissions on /var/run/mysqld should be set to u=rwx, go=rx, otherwise the socket connection does not work. I had to adjust them manually because the mysqld folder was installed with go-rwx.
Possible duplicate of bug 423387?
Try installing dev-db/mysql-init-scripts-2.0_pre1-r3 and see if you get the same result.
*** This bug has been marked as a duplicate of bug 423387 ***