If you don't have the little rubber trunk stop thingies, I'd suggest you get them and use Shoe Goo or some other strong rubber adhesive to stick them in place. You don't want valuable aluminum rubbing away, do you?
BTW, if the spoiler is tightly attached, the other culprit would be the trunk lid itself. When I first got my NSX, I noticed that the trunk would not close evenly - It was a little higher on one side than the other. While looking inside the trunk, I noticed something interesting.
As it turns out, the little rubber trunk stoppers inside the trunk actually screw in and out. With the trunk closed, look to see if the trunk is even. Then, push down on one side and then the other to see if either side is not actually seated. If the trunk is not firm on both sides, open the trunk and literally unscrew the little cone-shaped rubber piece that goes between the trunk lid and the body when you close it. Once you try it, you should know what to do.
Drop me a line if you have any problems with this. I was surprised not to see such a common problem and simple fix listed in the FAQ.
Aaron