It looks like there is some sealer (white)in your photos where the gaps are. That black rubber will continue to shrink with age making the gap bigger. Some times they pull away from the corners when they shrink. What I did was to push the rubber up to the top to eliminate the gap there then packed in butyl tape into the lower gap as shown in your photo. The tape comes in a roll and is the same tape you use to seal the windows to the sidewalls. It molds easily to the shape of the rubber and will seal better because there is no gap.