to start off, could you please provide a link to your webpage so I can inspect it directly? You can provide your link here or send the info to email@example.com if you do not wish to post it publicly.
Have you tried replacing the default Pulse favicon with your icon? Are you positive you put it in the right directory (root/templates/pulse/)? If you turn off your custom icon, do you get the default Pulse icon?
Furthermore, do you get any errors in the console? Such as 404, 50* errors on that file?
Please get back to me with more info so we can resolve this issue.