I saw a similar post back in 2013 but it was never resolved, So I am posting my own issue.
I am running my HTPC with a WMC remote receiver and a Logitech Harmony remote for control. My daughter was watching a show on live TV and Pause/ Stop/ Rewind and other functions from the remote wouldn't work. I have a wireless keyboard and mouse attached. I even clicked on the on-screen control buttons on the lower right had no effect. I was able to escape and at least get back to the main menu. Restarted the HTPC several times with no success.
I tried recorded shows and there does not seem to be an issue. works fine. I went back to live TV and the issue came back, but even then only on certain channels. Fox News and National geographic have the no pause/ stop/ rewind issue but CNN and other channels did not. I went back and forth between Fox and CNN several times and fox always had the issue and CNN would not.
Any thoughts or ideas would be greatly appreciated