My 360 spider also has this problem, however I cannot tell when or how it got like this as it was like that when I bought it. I just figured everything needed aligning. In my case the rubbers are installed but these are at the outer edge one on each side of the car. Not sure if there should be others or it is just adjustment on the hinge mounts?
Is there anywhere to get hold of how to set up the roof and panels?
Current Fcars: 360 Modena
Gone but not forgotten: 360 Spider, 575M, F430.
Other stuff: '71 Holden GTS Monaro, '80 BMW Alpina B9, '74 Porsche Targa, Caterham, MB CL500, Land Rover Discovery.