It would be unlikely for a hacker to have targeted your website specifically, I think. Mostly they will write a script that targets popular web software, such as vBulletin on TalkPHP. This allows them to exploit as many websites as possible, with the least research as possible. It could be that Lunarpages has a security issue regarding one of two of its scripts. I have a Lunarpages account for one of my websites, and I know they do send out automatic emails notifying you of any vulnerable scripts, so they are quite security conscious, it would appear.

The good news, I suppose, is that it's not so much a security hole in your application, but rather Lunarpages. Try contacting Lunarpages and tell them what happened. Hopefully they'll be able to advise.

Runar, in those handful of websites, did you check where they were hosted? If they were all hosted at Lunarpages, then we could narrow the problem down further. Otherwise it may well be that somebody has targeted your website specifically.

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