Syphoner isn’t a project we support. We build the underlying framework Syphoner uses. Please hit up http://www.sigmasix.ch/syphoner/ for help 🙂
Sorry we can;t be more help. Might be related to app-nap and the program quitting in the background? Maybe get info on the application file in /Application/Chrome and in the get info box -> disable app-nap?
Just a guess.