[stryderunknown]

From what I remember when I use to follow some exploits that occurred on a notorious site for logging site defacements. Usually groups don't just hack the individual website but actually obtain rights over entire servers (This was because there was a score system for how many defacements the groups obtained). They would exploit code that Host provider have installed on their systems and doesn't effect just one website but potentially their whole clientèle base.

If you can't find fault in your software or mods (If it's server side then they would rewrite the indexes as a BATCH), I would seriously suggest informing your Host or enquiring at the very least if they are having problems.