A tank of only 3ft, with no decor for obstruction of gunk, with good flow and a well positioned out take should be crystal clear.
Is it possible water isn't being fully filtered? It looks like from your pictures that the filter pads in your top tray aren't fully flush with the sides, looks to be a gap which could allow unfiltered water through your system. Also, it looks like water comes into the top tray from the side and not from the top. I think most would agree that water coming in from the top and filtering down maybe best.
Is your filter media fully intact? For example, i know of people in the past who have used certain types of pot scrubbies with a nylon backing to scour the dishes. This nylon backing can rot and bits become dislodged. I think it's probably something and nothing which is easily solved, a bit of tinkering here and there.