We ran into a similar problem where MySQL 5.6 was installed on an Xserve (instead of 5.5) and we had to take MySQL out of Strict Mode.

NOTE: The JAMF docs say to install MySQL 5.5 or later but in recent discussions, we've been told that 5.5 is the "last stable" version and 5.6 has some issues:

external image link

Can you post your /etc/my.cnf?

PS, the environment was inherited, not sure why MySQL 5.6 was installed if OS X Server already has MySQL.

<shrug>

HTH
Don

That warning is just that, a warning. Does the error say something like 'MySQL server has gone away'

Also are you trying to use a mysqldump by any chance? If you're trying to restore from a mysql dump you probably need to either increase your maxpacketsize or your timeout.

@Chris_Hafner Late but relevant...

https://jamfnation.jamfsoftware.com/discussion.html?id=4973#responseChild50726

That one is a good thread. Someone will need it here at some point!