Can't connect to MySQL + other ?'s

#1
A client of mine has a small joomla site thats been working fine for a couple of months - I happened to view it a couple of days ago. Yesterday I get a ticket saying: Database Error: Unable to connect to the database:Could not connect to MySQL

I managed to fix it by adding a new user/pwd to the db and changing the config.php. But I'm wondering why this would happen for no apparent reason?

It seems since upgrading to the Hybrid I'm experiencing random but annoying issues; like:

the /root/cpanel3-skel permissions keep changing so that domains can't be viewed using ~username and it also results in new accounts failing to be created properly.

permissions or something for cron jobs keep changing and my cron jobs stop running.

I'm running Automatic (STABLE tree) 11.24.4 of cPanel and 11.24.2 of WHM

Could the cPanel updates be breaking stuff?
 
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