If this is only happening in one particular song, try going into Documents>Studio One>Songs>Your Song Name and delete the folder named "Cache." Do this with Studio One closed and then re-open the song.
You will also want to make sure that you have installed the latest version of Universal Control and that the firmware is updated. Here is a link to our downloads page if you need the latest version.
http://www.presonus.com/support/downloads
You will want to open UC and verify that you have not changed any of your Aux. Routing.
Finally, if you have added the Console Shaper to your master track in Studio One, try turning off "Crosstalk."