They appear to be identical content, but they are really just the same page. I give a special URL to my affiliates to track their sales. Previously, Google could tell the difference, but it seems something has changed. I've had this problem for a long time with Inktomi. I just thought Google was smarter.
We also had this problem with our affiliate system, as each page looked like an ordinary .html page (i.e. with no special characters), which resulted in quite a bit of what google thought was duplicate content being indexed. The good news is that it was easily solved by having our system add a no-index robots meta-tag to all affiliate-referred pages.