CphD

Depends on how you define "major." http://forum.utorrent.com/viewtopic.php?pid=722250#p722250

Nice catch.

It's a bug, but the workaround is to pause first (via context menu since the pause toolbar button was removed.?!) and then they can be stopped.

No, it's possible if you install each following prescribed procedure. From the description I suspect the alpha version overwrote the stable version .exe file in Program Files. That .exe file is still using AppData folder settings info (settings.dat). Determine which version will be portable and which will be standard installation (i.e. Control Panel Add/Remove). See http://forum.utorrent.com/viewtopic.php?pid=705506#p705506 about setting up a portable (encapsulataed) installation after the standard install version. On the portable, copy those .dat and .torrent files into a new portable directory, move and launch the installation file within that folder, create a shortcut and it will be self-contained.