I have set (in Waterfox) Waterfox as my default web browser but if I click a link on an e-mail or even on a site while using Waterfox my Firefox starts to load the link as tho it is the default.
Go to Solution.
Uncheck the Firefox Default browser in
Tools > Options > Advance > General > System Default > Always check to see if firefox is the default browser on Start up
Check the option in Waterfox
You may need to check the related registry keys in HKEY_CLASSES_ROOT to verify that they link to Waterfox.
Also make sure that Firefox isn't running in case the Waterfox startup code detects an open Firefox instance and uses that.