If that's with just a certain system or some, make sure the software-lists in question are enabled (click on the icon in the tool-box header's top-left corner, select "Visible software-lists" and then follow the menu - see here)... if that's with all systems, then clear the software-list cache and let it reload software-lists.

The software-list favorites are stored in the "user-data database"... if the software-lists they are from are set to invisible they aren't shown, though.

A mind is like a parachute. It doesn't work unless it's open. [Frank Zappa]