I too have to keep the tops motor running as I pull w/ the center "hand hold" before I can latch mine. It is a bit of a pain. Interested to hear if that fixes yours.

 

The drivers side pin goes into a hole in the header, but if you look close, the pass side pin hole is realy a slot. This means you MUST latch the drivers side 1st! or it may latch out of alignment. I have had mine since early March and I had all kinds of trouble with the latches until I figured this out. Hope this Helps.
Rick

 

Update:
Dealership replaced both the latch mech. with the pins in the top, as well as the recepticles in the top rail.
Now top comes all the way down and touches top rail iwith both pins in alignment with holes and with one hand, minimum pressure in center hold while engaging latches. Works like a dream. Just in case anyone else has difficulty with Pin alignment
Kurt