I use WordPress myself and have heard of incidents where people have had file changes/hacking (not sure if that is the case here though).
It may be a really silly question but have you made sure you're using the most up to date WordPress as usually it prevents this sort of thing happening. I've known someone who got hacked regularly and it stopped when he regularly upgraded. He only ever upgraded when it was 2.x rather than 2.x.x.
Just out of interest, what version of WordPress have you got installed?