When I try to add a new group it gets added inside that last group at the bottom of the script list. I can't move it to the left to get it out of that group. Same if I try to add a script or separator. Is anyone else having this type of problem? It seems quite flaky.

This actually a little bit of a funny interface issue. What's happening that the group at the bottom of your script menu that is open. Now, whenever you add something it just automatically starts out in the group. You can get it out if you select the up down arrow of the script/group or separator and slide it about the Group. It's a little finicky but you can get it out.

It definitely sounds like you found a bug though. I wouldn't want new items to automatically appear in a folder if it happens to be at the bottom and open that's for sure.