Repeatedly "trying to add a new helper tool" on each restart for same application(s)
Try changing the ownership of Atom.app. In my case, Atom.app was found in /Applications, and ownership was:


  drwxr-xr-x   3 1699963712  365896978    102 Dec  8 12:48 Atom.app


I ran the following command:


  sudo chown -R $USER:wheel /Applications/Atom.app


In my case, any program with ownership of root or the numeric code listed above would have a popup a few seconds after opening. Changing ownership of the .app directory corrected the behavior and I don't see it anymore.

I found the information at this site.