I have been struggling few days because my chrome for some reason didn't open magnet links. So my final solution was:
Uninstall Google chrome
Delete C:/Users/username/AppData/Google
Delete C:/Program Files x86/Google
Then download and install Google Chrome again.
Open search and type: regedit
find: HKEY_CLASSES_ROOT\Magnet\shell\open\command
and set path for your torrent software.
This did the trick for me. Some users might need to check this step, but this should be unnecessary to do after full reinstall of chrome.
Go to start menu > run
type in %LOCALAPPDATA%\Google\Chrome\User Data
Double click the Local State file
select notepad to open it.
search for "protocol_handler" > "excluded_schemes" > "magnet": true
Change true to false.
