Are you using the FullyRouted servers or the Proxied servers? There's a few ways to prevent this, one is to use our Proxied servers and configure proxy settings in uTorrent. This prevents uTorrent from going through your own IP instead of our servers.
If you're on Windows and using our BolehVPN-Gui, I believe there's a protection feature where it will freeze all traffic in the event you suddenly get disconnected from our server. So use the fullyrouted servers with our GUI.