Updated to v. 1.06. Only change is it kills it's own tray icon before calling the Tray Refresh function. This should improve cleaning off dead icons. Note that if you quit RunGroup via the Tray Menu it does not kill any of the apps it launched or clean the tray menu. It just kills its own icon then quits.
edit: just more info, the "Tray Refresh" function that cleans off dead tray icons is just a function written by one of the programmers on the AutoIt3 Forum that moves the mouse over the tray to simulate doing it by hand to kick the dead icon off. Since it moves the mouse I'm not sure if your chances of cleaning the tray are better or worse if you happen to be moving the mouse yourself at the same time. It's just a macro thing and won't work in every case.
Just from messing with it myself, the way I have it set to call it twice with a pause in between, it seems to work at least 90% of the time. I get the impression maybe one out of 20 it will leave my GigaGet dead tray icon still visible. Not bad for a macro gadget.