this simply does not happen to me....C1 does not process or change the files in any way....all files in C1 have some profile, settings, curve,....attached....
are you shooting tethered? if not try it and take a shot, attach profile, settings, color, curve,....now send the settings to the back and every shot coming in or to your card will have these settings....
there really isn't much you can set on the back when shooting ot card, but you can send any setting to the back and the back will continue to shoot with these settings....
in a way we never see the raw file...we only see the raw file with the settings attached that we choose....maybe you have some profile attached that makes your files look so wrong.....LR cannot read the phase profiles, so the file would look very different in LR.....same for me...but the difference is in color, saturation,...not exposure....