As stated, you cannot use inputs that pause processing of events ($?="" and $input) in events that pausing the processing of the event would be detrimental. Some events, they work in, many they do not. I can't list all events that work or don't work, but it's easy to just check and see if it lets you do so by testing it in the event. If you get the error, then you can't use it there.
Also, as stated, the workaround is to use a timer...
.timer 1 0 var %question = $?!="Shall I continue?"
That said, a much better solution for what you're trying to do would probably be to use aliases. Stick the var line into an alias and put the processing information in the alias as well. Then just call that alias from the main script. Besides being nicer than a timer, this also helps organize your script. You would now know that the alias handles the processing of the script after the question is asked.
