I recently backed up my WP site using a competitor utility BackupBuddy. Upon restoration, I kept getting this error: MySQL has gone away. After much research, tweaking PHP extensions, trying different versions of PHP, patching MySQL, and trying different versions of BackupBuddy, I was still getting the error. Then I decided to check the status log that BackupBuddy creates. There I realized the last query being and executed on the database restore was from the [prefix]_options table with a option_name of wphb_scripts_collection.
At that point I thought perhaps it wasn't a bug with BackupBuddy or my setup. I attempted to perform a MySQL dump and restore (not using BackupBuddy). I still got the same error. Then I removed that row from the backup file. I was able to restore the database without error both manually and using BackupBuddy.
I'm not sure exactly what MySQL didn't like about that record value, but something in the object cache has gone awry. I just thought I would pass this along.