The correct point is in the root directory of the template folder.
Have you ever deleted the Joomla cache or the browser cache? Have you tried another browser before?

I consistently clear out the cache whenever I make changes in the backend. That’s not an issue. It doesn’t matter if I’m using Safari, Firefox, or IE. It’s the same for them all. Thanks for the tip tho.

Which favicon is displayed on the startpage ? That from Joomla?

Yes

Hello

The root template folder is the correct location to place a custom favicon. Most likely this is a cache issue, most browsers will continue to load the first favicon even after clearing the browser cache. Have you tried loading your site in a different browser since changing your favicon?

Ciaran

I think you're right. I noticed just recently it only appears to be an issue in safari on my iPad. I'm not going to worry about it. Thanks for the responses.