Sorry to hear that. Such hacks can happen via lots of way, Server itself, the ModX hack you mentioned, a plugin, a custom theme…
There was no security fix in 1.4.13 otherwise it would have been noted. There are no actual security issues known to us currently. But that of course never means there might be one somewhere. Nothing is 100% perfect ever.
Please mail me directly via our contact form so we can talk about this directly.