I think the point that everyone is missing is that he can't automate pushing the "Ok" button after MalwareBytes updates. I'm having the same issue. Whenever the MalwareBytes window is active, all of the AutoIt keyboard and mouse commands stop working, so it becomes impossible to interact with the window. The whole point to automating a MWB scan is to not have to push any buttons after starting the script, so having to click "Ok" defeats the purpose. I don't know why MWB is being weird like this but it seems to be an compatibility issue between MWB and AutoIt.
