What about the output of 'show processlist'?
On your server that runs the cron process, check for any PHP processes which are hanging around, eg: ps fauwx | grep php
You may find that your cron scripts are hanging around for a long time, holding DB connections, possibly locked on something like stats processing. You should kill the old cron processes to free up the DB connections, but first check the 'show processlist' to see which queries they are blocking on - this will give you a clue as to where the bottleneck / lock lies.
Hardware and performance
Connection limit reached?
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