just as when opening the top, when closing you need to keep pressing the button until the light goes off. Though it may 'look' closed and even latch, it's not until it's fully cycled and the light goes out.
O.K., I continue until the light goes out (I feel dumb for missing that one) when putting top up. Everything latched good, light out on dash, but when I open the door the window drops then goes right up when I let go of the handle (still).