OK, I think I figured out why.
I removed the Default Init Tool from the game settings because I didn't think I needed it since I also loaded Init Tool Default D&D.
Jay, if we need Default Init Tool for InitTool to function properly, I wouldn't allow the user to delete it. Actually, I probably wouldn't even have it on THAT list at all; either hard code it or if that will screw up with other game systems, put it on a different list all togehter.
I can see people deleting it after loading the D&D list like I did. Maybe you can append the needed default name with (Do not delete this rule)
You do not need Default Init Tool. It is there for people who aren't running a D&D encounter. When you do switch game settings it does create a new encounter and a new group, since the properties are not likely to be the same between different games. If the encounter was a new one or had been changed it should ask you if you want to save it before it clears it. If it does not, that is a bug.