Earlier today I was informed of a few minor security problems and one very dangerous database backup risk. The minor problems are easily fixed, download the file 4.01 Security Fixes from the Downnloads area (PHPFusion Core), and replace your current files with the new ones.
As for your database backups, you are advised NOT to keep your backups stored on your server, instead download the file to your computer and delete the file off your server. Alternatively, rename your db_backups folder and edit the line $dbbackupdir="$admindir/db_backups/"; (replace db_backups with the name of the folder).
The Full Install and Upgrade packs have been updated to include the fixed files.