[MrAd]

there are a few ways to hack into a board/server.
is your webspace really empty or is there still one file, which you dont know? If so, it´s maybe a shell which the hacker is using. Make sure your ftp-client is able to show you .ht files, which are normally hidden, otherwise it can happen that you dont see anything, but there is a file.
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change your username for your ftp and/or controlpanel. Look for security patches for your board and install them (if there are any patches avaible). Check if the php-version is up to date. If not ask your hoster to update it or patch it.
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To list all possible ways to hack into a board would burst the topic.