I'm running Xubuntu 13.10 and have set inactive windows to be transparent. However, is there a way to prevent one window/program (i.e. tvtime) from becoming transparent.
You'll need to play a little with compiz to get this. Install compizconfig:
And under the Windows Rules section you'll find this rule: "No ARGB visuals". You need there a way to identify your window, either the title, class, etc: