"running unsupported mysql version" even after upgrade

Last night I upgraded mysql from 5.1 to 5.5 and then 5.6 and now some of my clients are having problems connecting to their DBs.
For instance, when I try to force-change their passwords through WHM and sync their DB password, i get the following error:

Code:

Password for “XXXX” has been changed.
Updating FTP passwords for XXXX
FTP password files updated.
FTP vhost passwords synced
Error from MySQL query: DBD::mysql::db do failed: Lost connection to MySQL server during queryError from MySQL query: DBD::mysql::db do failed: MySQL server has gone away

I checked my.cnf and for what google tells me, it seems like I shouldn't be getting that error.

Code:

[mysqld]
innodb_file_per_table=1
innodb_buffer_pool_size = 384M
innodb_additional_mem_pool_size = 20M
innodb_log_file_size = 10M
innodb_log_buffer_size = 64M
innodb_flush_log_at_trx_commit = 1
innodb_lock_wait_timeout = 180
open_files_limit=50000
max_connections=500
max_allowed_packet=128M
wait_timeout=600

Trying to open the mysql databases through the client's cPanel shows the following error.

Code:

This server is running an unsupported MySQL version (Error while connecting to MySQL: Cpanel::DBI::Mysql connect('','root',...) failed: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2) at /usr/local/cpanel/Cpanel/MysqlUtils/Connect.pm line 136 Error while connecting to MySQL: Cpanel::DBI::Mysql connect('','root',...) failed: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2) at /usr/local/cpanel/Cpanel/MysqlUtils/Connect.pm line 136 ...caught). Ask your system administrator to upgrade MySQL to improve security and features.

But mysql seems to be running correctly with newest version.

Code:

mysql -V
mysql  Ver 14.14 Distrib 5.6.17, for Linux (x86_64) using  EditLine wrapper

I've tried both /scripts/check_cpanel_rpms --fix and /scripts/upcp --force but the problem still persists.

Also, some client's domain doesn't seem to be resolving the DNS at all, even though every DNS entry seems to be fine and unaltered.

Code:

>ping XXXXX
Ping request could not find host XXXXX. Please check the name and try again.

Google hasn't been of much help so far. Any suggestions?

 

CentOS 5 running under Xen.
Not sure about the MySQL Governor, but if I had to guess I'd say no.

 

Ticket ID 5658101
I've been awaiting for a representative for about 5 hours now, hope I get a response soon. All the clients on the server are down in the meantime.

 

Yes that solved it, thank you very much.
Domain names still weren't being resolved, but restarting nsd did the trick.