Yeah, I kind of figured that but I see no way to load a default list.
You have to use the Open button while you have the correct Game Settings file selected in the list.
I currently have nothing in my list at all - do I need to manually add them all?
Nope. Just do the above.
Also, could this be the reason why I do not see any custom properties for the D&D lookup monsters?
Yes. Until you have a list of Custom Properties the Add Combatants dialog doesn't know what properties to display.
It shouldn't be affecting you but you could delete all the old prefs stored in the registry.
Close IT and use regedit to delete this key and its subkeys:
And of course deleting the .inittool folder under C:\Documents and Settings\<your username>\
That would take you back to a new user experience.