I had this problem, couldn't fix using the tool, couldn't fix "manually" via associations. However, I was able to make Iron (Portable) my default browser on two computers both running windows 7 by making IE the default then making Iron the default. It's probably not the "cleanest" (because you'll leave some IE defaults in place), but all links work and stuff opens Iron automatically -- so it's at least a good starting point.
1)Make Internet Explorer the default browser using the Default Programs control panel
-- Start Menu
-- Click Default Programs
-- Click "Set your default programs"
-- Click on the Internet Explorer icon
-- Click "Set this program as the default"
-- Close the window
2) Make Iron the default browser inside Iron itself
-- Open Iron directly from the .exe
-- If it asks with a banner "Iron isn't the default browser...", Click "Set as the default" or "OK"
-- If it doesn't ask, set it as the default using the settings.