Which WHDLoad list? AGLaunch, List Launcher or iGame?
Since you asked about AGLaunch and mention the addgame scripts here:
http://eab.abime.net/showthread.php?t=62685
...I'll take a guess it's not finding all your games. The AddGames script will add all installed WHDLoad games to the List Launchers IF they are in the the drawer/partition path listed under the A-Games: assign (default is SYS:Games).
You can change were it looks for games in the S/Assign-Startup file, where A-Games: is listed. If you are using the LITE and below versions, this file can also be edited using the right click pop-up menu Workbench->Startup->Assign.
This vid (top one) shows the file being edited at about 1.02 :
http://classicwb.abime.net/classicweb/tutorials.htm
Hope this helps.