That's a good point - I too have HDMI from the STB to the TV and use the component to S-video to the tv tuner card.
I thought I had unplugged the HDMI cable during my attempts to troubleshoot, but will give that another attempt.
In terms of the component to s-video, I have been using that connection since I switched to Fioptics in March, 2012. I had no issues until this recent patch was pushed out. Tech support was absolutely useless in trying to fix the problem.
I was considering upgrade my tv tuner to a Hauppauge WinTV-HVR-2250, but I wonder if I would be better off choosing a PVR model instead. I use Mediaportal TV Server to record, and view through XBMC.