your internal strengthing bars are bent/warped. it involves taking the inner vinyl and insulation off to get at them but what Campershop do to repair the center section before fitting the rubbers is to derivet/rerivet them all with new and add triangular corner pieces to the bar to give them even more strength. they also supply a strong stickyback black durable cover to go over the outside on the top of the center section. This adds another barrier to the rain.
This is the weakest part of the whole mechanism and as its up and down all the time over time the rivets get loose the strengthening bars warp and water will leak through loose rivets into the bus. I think you need to sort out the warp before you will get a tight seal on the skylight unfortunately .