In terminator version 0.95, this issue still exists.
Having a look at the python code of terminator, it seems that when one right-clicks and chooses menu-close, the terminal is only deregistered by calling the method deregister_terminal from the terminator class. Adding the line "terminal.close()" before it is removed from the terminals list (at "self.terminals.remove(terminal)") seems to solve the problem for me.
In terminator version 0.95, this issue still exists.
Having a look at the python code of terminator, it seems that when one right-clicks and chooses menu-close, the terminal is only deregistered by calling the method deregister_terminal from the terminator class. Adding the line "terminal.close()" before it is removed from the terminals list (at "self.terminals .remove( terminal) ") seems to solve the problem for me.