Stallion, do you have the factory t-top covers? If they're like mine, the back side of the snaps are exposed on the inside of the bag. That might be what scratched the tops. Go to Lowes/Home Depot/equivalent and you can find little green felt circles with a peel and stick backing. Use these to cover the back of the snaps where the exposed metal touches the tops. The little felt circles are made to stick to the bottoms of lamps and such to prevent scratching glass or marble coffee tables etc. Should only cost a buck or two. You could even buy plain felt without the sticky backing and super-glue it on. That might even hold better - that peel and stick backing doesn't always hold - it softens up and slips around sitting in the sun inside a hot car.
Let us know how that stuff Dave recommends works if you go that route.
Dave - does it really do what the web site claims?
Semper Fi,
Culprit