You may have already tried this, but I would check your "Audio I/O Setup". You can reach that menu two ways: (1) from the drop down under the input on any track, or (2) in the "Options" menu (under Studio One) select "Audio Setup" and then "Song Setup". Ensure that the inputs you want to use are there (you may need to click "add" mono or stereo inputs) and then activate them (a letter "M" will be displayed in the square that corresponds on the inputs matrix). See photo below. I hope this helps.