Mysqld random shutdown

I'm having an issue with mysql similar to this post: http://forum.centos-webpanel.com/mysql/mysql-auto-shutdown-at-night/

Until the version 0.9.8.20, mysql has runned uninterruptly for hundreds days. Now it's stopping randomly at night, some night it stops some other not. I've tryed “chkconfig mysqld on”, i've disabled mysql backups, but the problem is still there.
I can reproduce the issue by launcing the following:

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/usr/local/cwp/php54/bin/php -d max_execution_time=1000000 -q /usr/local/cwpsources/admin/include/cron.php
and then

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service mysqld status
tells me

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mysqld dead but subsys locked
 but if i restart mysqld and relaunch

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/usr/local/cwp/php54/bin/php -d max_execution_time=1000000 -q /usr/local/cwpsources/admin/include/cron.php
mysql do not stop. It seems like in cron.php there is some operation that will be executed only once in a while... if i wait some time, from hours to days, then the launch cron.php leads to mysqld stop

Mysql log relevant part:

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161007 15:04:24 [Note] /usr/libexec/mysqld: Normal shutdown

161007 15:04:24 [Note] Event Scheduler: Purging the queue. 0 events
161007 15:04:26  InnoDB: Starting shutdown...
161007 15:04:28  InnoDB: Shutdown completed; log sequence number 18166463123
161007 15:04:28 [Note] /usr/libexec/mysqld: Shutdown complete

161007 15:04:28 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
I'm experiencing this issue in all my servers which are running mysqld 5.1 and also others which i've upgraded to mysqld 5.5
I need some help to solve this bad issue.
Thank you

I'm having the same problem... :/