With the switch to Squirrel.Windows (or with SourceTree 2.0.x, I don't remember the exact time), URL:sourcetree protocol links stopped working. This in fact means, that the "Check out in SourceTree" links from Bitbucket are not opening SourceTree anymore.

It seems like the sourcetree: protocol is not created/linked with SourceTree anymore. If I manually change the protocol association, it works again:

[HKEY_CLASSES_ROOT\sourcetree\shell\open\command]@="C:\\Users\\USERNAME\\AppData\\Local\\SourceTreeBeta
Update.exe --processStart \"SourceTree.exe\" --process-start-args \"-url %1\""