You didn't fix and nothing was wrong with the database. Error: 2006 - MySQL server has gone awayThat means the mysql setup is not tuned for your vps correctly. This will continue to happen intermittently until the setup is optimized for you.
Thanks for posting your solution too! This is a weird thing though and i haven't really seen this happen before. The question(s) in this support topic have been answered and the owner has been able to solve the problem. Because of this, the support topic has been closed and moved.If you have other questions, please open a new topic.