I have a '97 328 ic. When I drive with the top up faster than maybe 55 mph, the rear window flutters or shakes. The top's bottom seal moves back and forth an inch or more.

Is this normal? Can anything be done about it?

the window shaking is normal, the seal moving is not. sounds like something is loose or not attached properly. i would start out by tighting all the fittings in the frame of the softtop. its probably a good thing to do occasionally anyways, and you might find the problem as youre looking around in there.