What type of source are you using to capture your desktop? From your explanation I would think you use either a Game Capture or Window Capture on the League client?
You will probably want to use different scenes for League and for your Desktop, use a gamecapture for league and either Window or Monitor capture for whatever you want to show on your desktop.
If nothing helps, show us a log file: Problem? Make sure to post a log and/or crash dump -- HOWTO
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