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I went to put the top down on my 96 and it didn't want to fold down all the way. It has always folded down so the tonneau would close with minimal effort.
I fiddled with it for half an hour and determined that for some reason I have to reach under the window and help it up on the shelf for the top to fold completely.
I can't figure out why it suddenly started doing this. Nothing appears to be wrong.
make sure you start fresh every time, meaning put the top like it is up, then lift the back up, and start to pull the front up and back with the top, it should fall right back in to place.
Make sure the glass rear window isn't trying to collide with the top bow above it. I've noticed lately that my '94 rear window seems a bit uncertain as to whether it wants to stow below or above the nearest bow (I've been "helping" it make sure it ends up above that bow). Could be what's going on with yours. Look very carefully everywhere else for anything that's binding, or any stray items that might have ended up where they could interfere with the movement or stowage of the top.