Judging by the pics it appears that the rear flares up near the bottom and if that's the case then I would have to agree that your particular top has a problem. I have the same model of top and those rear pieces hang straight down with no flare and subsequently fit perfectly into their respective slots.
I will suggest before you call Bestop one more procedure and its how I found to be the easiest way to put the top up on my jeep. I start with locking the soft top frame into the middle locks near the door frame first. Next lock in the rear corners. Put one hand on the top of the rear frame and pull down then slip the plastic tabs into their grooves. Lastly, lock soft top frame into windshield and I stress doing this step last otherwise there is not enough play in the frame to pull down the rear flaps.
Just another thing to try and I hope I explained this clearly.
If that doesn't work call Bestop and surrender