I'm no expert on RSM setups, but there is a dedicated forum here, I'm surprised there haven't been any RSM experts chiming in...
All tanks water levels fluctuate by evaporation, and I'm not sure where the RSM will show that, but it sounds like you have more flow resistance (yes maybe media?) or debris on that side. It's also possible the two pumps are not perfectly in tune, but I would clean out the media chamber and make sure it's not getting clogged.