Heidrich, I was on phpNuke when I was brutally hacked and from the way it is being described, my attack was similar to yours. One thing I took note of was SSH traffic. I had previously been hacked once before, a minor defacing, but I made note of the SSH traffic on that as well. This time it was much larger. It was then I requested my SSH and telnet disabled - in fact, all avenues of access other than ftp and http closed. Knock on wood, I've not had anything happen since. It was this last hacking that I had decided to move to vbulletin - away from phpNuke. Fortunately, since I worked for my ISP, and we were going to migrate to a newer box anyways, I built our next hosting box. The crack had corrupted the old mysql database. Even recreating the site wouldn't fix it. I hope your fix is easier than mine was.
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