Ive actually encountered this a few days ago.
After some research we concluded that the message is reported when the mstest runner does not ends properly.
In our case it was caused by the application code, and we manage to fix that with no relation to Isolator.
I'm guessing that if this just started to happen after the upgrade to 6.0.1, you should wait for the mentioned patch.
:| just thought to add some additional info