Sep 29 21:55:37 Tower emhttpd: cmd: /usr/local/emhttp/plugins/dynamix/scripts/newperms /mnt/cache|/mnt/disk1|/mnt/disk2|/mnt/disk3|/mnt/disk4|/mnt/disk5|/mnt/disk6|/mnt/disk7|/mnt/user/appdata|/mnt/user/Books|/mnt/user/Dell Windows 7 Data|/mnt/user/Documentary|/mnt/user/domains|/mnt/user/Home Video|/mnt/user/iPhoto Library|/mnt/user/iPhoto Library 1|/mnt/user/isos|/mnt/user/Kids Cartoon|/mnt/user/Macbook gloria backup|/mnt/user/MacbookProBackup|/mnt/user/Movies|/mnt/user/Music|/mnt/user/Music Video|/mnt/user/Network Trash Folder|/mnt/user/Pictures|/mnt/user/system|/mnt/user/Temporary Items|/mnt/user/TimeMachine|/mnt/user/TV Series|/mnt/user/Videos
Based on this, you selected both All disks, and All shares. Effectively that means that it's going to run twice. Not a real issue though.
On the popup that appeared, did you see any text as it went through and did its thing (disk 1, disk 2, etc)