I imagine that when you installed JMR you chose to have JMR installed as a torrent client.
Uninstall and reinstall with that off or alternatively simply change the file association.
Control Panel > Programs > Default Programs > Associate a file type or protocol with a specific program
Search for magnet, double click and set it to what ever app you want.
Jaksta has taken away file associations from my torrent software and does not function. I did not choose to lose these file associations and my ability to torrent has been destroyed.