program stalls, is non-responsive, but its running process cannot be killed with taskmanager

A strange and annoying problem that seems to affect mainly bittorrent apps
but has also affected Explorer.exe.

I initially had it happen with Bitcomet.. the program stopped responding for
whatever reason and wouldn't close with the Windows pop-up. Task Manager
also couldn't kill the process and the program window just remained
on-screen. Only a reboot would get rid of it. Thinking it was a
program-specific problem I uninstalled Bitcomet, but as it happened I get
exactly the same problem happening with both Azureus and uTorrent. The
stalled program doesn't affect other software that is running but ports that
it opened remain open and also cannot be closed.

In one instance since this started I also had an explorer crash that did not
recover on its own. After I restarted explorer.exe manually from Task
Manager I found that there was an existing 2nd instance of explorer.exe
running. It was non-responsive and the process could not be killed. As with
the bittorrent clients I had to reboot in order to get rid of the
non-responsive program.

Anyone have any idea what is going on here?