It's GoDaddy not vB.
I had something similar happen a couple of years back with another type of site. The site ran fine for nearly 8 years on a dedicated server, but due to the economy the owner decided to move the site to GoDaddy to save money. Within one month of the move the site was hacked in a similar manner. It was not hacked with FTP, or by obtaining any of the site passwords. It was hacked directly from root access to the server. The site was immediately moved back to a dedicated server under my control and the site has never been hacked since.
Despite what they say, in my opinion GoDaddy does not secure their servers very well. That's entirely my opinion and not intended to bash them.
But keep in mind whether on a dedicated server or a shared server, security is always the responsibility of the site owner not the provider.
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