Each favicon is in the same directory as the page giving the <link rel> tag? When you look at the HTML page source in your browser, does it show it's looking for the favicon in the right place? Do you get an error log entry that favicon.ico is a 404 for certain browsers?

Since you are using the default name and type (favicon.ico), you might try simply placing them in the main domain root / and the add-on root /addon respectively. That's where browsers will look if not otherwise instructed with a <link rel> tag. You should need the tag only if you have a different file name or non-default location.

Different browsers can be squirrely about picking up changes to favicons, once they've recorded them. You might have to clear your browser cache, or even remove the site and put it back to favorites/bookmarks to get the new information to "take". Even a first visit to a site can work in unexpected ways, with a favicon not showing up for days sometimes.