Here's an answer you might not expect. I had encountered the same problem. MySQL Error 2013. Here are the symptoms:
PHPMyAdmin fired off 2013 and error 95.
I could shell into the MySQL monitor, but it took an inordinately long time to start. I could view tables and everything worked once the command line utility started
The server took a LONG time to stop and restart.
No errors in the MySQL error log.
I work with a good sysadmin who checked netstat -tn, which yielded the answer:
tcp 0 0 [my.srv.ip]:3306 184.73.87.215:59271 ESTABLISHED
tcp 0 1 [my.srv.ip]:38138 184.73.87.215:113 SYN_SENT
The IP resolves to Amazon Web Services. Some prick was leeching onto my 3306, even though everything but port 80 is allow-only. It's time to review my firewall rules.
There were no new tables, and mtop didn't show any activity, but I found a ton of these in the auth log:
Apr 19 15:14:52 magic2 mysqld[18953]: refused connect from ec2-184-73-87-215.compute-1.amazonaws.com
Apr 19 15:18:02 magic2 mysqld[18953]: refused connect from ec2-184-73-87-215.compute-1.amazonaws.com
After blocking the offending IP in iptables, the problem suddenly went away. Sneaky Bastards. The moral of this story is: What looks like bug, might be a hacker.
bz