I'd have thought it's likely that something is fouling the lid on the inside - am assuming you have tried closing it with no duvets, matresses or whatnot in the bed area to rule this out. do your scissor/lattice brackets look to be parralel and in line with the van - when closing if they bow in or out it could potentially mean they don't close fully /correctly.
Also a small child in the pop top could potentially case this also - try jumping up and down on the roof if this is the case
Hope you can get it sorted