2. Security permissions
Those kind of pop-up windows are completely normal.
You need to give access to maScriptRunner to talk against other applications.
In this particular case you need to give access to maScriptRunner to run Applescripts, what is the main reason to run maScriptRunner.
Only Applescripts that are stored inside a folder that you defined within maScriptRunner.
IMPORTANT: If you applied "auto restart" in the preferences panel of maScriptRunner, you need to give access to maScriptRunner to restart himself.
MaScriptRunner will not execute or interact with other applications as long as you do not give permission to do so.
(!) REMARK: Those kind of permissions must be given only once, on the first run of maScriptRunner or a particular script.