Yes, I had that problem...my old top fit fine and the newly refurbished one did not. It as way too tight (seemed too long) to fit properly. My top was rebuilt by a professional well known for it.
Try measuring across from front Driver's side location vertical pin receptacle to the passenger side rear horizontal pin receptacle and then do the same for the other direction (these measurements make an "X" across the top of the targa opening on the car). Mine was off close to half an inch from one side to the other. I ended up have to remove one of the front vertical pins to be able to mount my top. I mounted it in and latched it closed months ago hoping that it would self heal. Time will tell.
My measurements:
My car was in an accident 10 years ago which hit more on one side of the front bumper which probably accounts for it.