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pure-ftpd in verbose (debug mode), it was complaining about database, so I created the database for it, and the table.
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Please undo that as your setup conflicts now with ispconfig.
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But then I create users in ISPConfig they are not added in the database.
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Your pure-ftpd connects to the wrong database. the ftp users are stored inside the ispconfig database and pure-ftpd connects to it.
I guess you installed or reinstalled pure-ftpd after you had ispconfig installed and that remobved the correct pure-ftpd configuration. To fix that, download the ispconfig3 tar.gz file again, unpack it and run the update.php script. Choose to reconfigure services during update so that your config files get fixed.