I can't replicate this problem myself with either CodeRunner 3.4 or 3.5 (just released). It used to be a problem with an older version of the Ace Editor but was fixed in mid 2016 by upgrading to the latest Ace editor. The version that comes with CodeRunner 3.4 and 3.5 shouldn't suffer from it.
Is anyone else experiencing this problem?
How long have you been running CodeRunner and how long have you been seeing this problem? What browser are you using and have you tried other browsers?
I suspect you are running an old version of Ace - perhaps cached somewhere? - though I don't see how that could be happening.
Sorry but I can't fix something that I can't replicate myself.
PS: I also don't see why this is "very urgent". We lived with it for years with an older version of Ace. You just have to learn to click somewhere in the window after the Check.