There is a bug in Media Foundation on Windows 8.1. It's simple to reproduce, including in Topoedit.
Steps...
-Add a video capture source (we've tried several - including the AVStream Simulated Hardware Sample)
-Add a EVR
-Connect them
-Play/Run/Start (observe that you get video)
-Stop
-Play/Run/Start (observe that you don't get video)
This was not a problem with Window 8.0.