maScriptRunner is entirely Apple® sandbox compliant.
If you like to know more about Apple® sandbox technology, go to:apple.com
Those kind of popup 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.
Afterward, the system knows that you trust maScriptRunner.
We suggest to code sign your own Applescripts to be compliant to Apple's security standards, therefor you need an Apple Developer ID.
How to do this: Is clearly explained at: