How weird! I think whenever I expressed both sides got mixed together so I could never compare. I'm guessing the fat/water ratios must be different with the different volumes and maybe the difference becomes more obvious when it freezes (cause EBM always looks different frozen and defrosted as opposed to room temperature). I remember reading once that if you have oversupply you essentially have the same amount of fat in each feed as a 'normal' supply, it just get diluted with a whole lot of extra water which is why babies can drink and drink and drink the oversupply and still seem hungry....it's like skim milk! So maybe each side has the same amount of fat but more or less other stuff which gives it a different appearance?? Not saying you have over supply, just a varying supply with varying ratios.
An interesting experiment - if you had some spare EBM - would be to leave some from each side in the fridge for 24 hours and see if the ratio look vastly different once it has separated and the fat/water is easier to see.