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I found today on google that a supplemental listing in the form www.mysite.com/default.asp?affilliateid=XX is returned on the site: search and that if I search on 'mydomainname', that this page actually ranks higher than our proper homepage. I also ran the link: search for the affiliate page and it returned the same backlinks as the regular homepage (whereas plain www.mysite.com/default.asp does not). So I suspect that this may be the source of our problems (or at least one of them).
The site that is using this very outdated affiliate link (from circa 2003), I frankly wouldnt want to let know that our site could be caused problems in such an easy way (since us not ranking well is helpful to their own rankings).
So what I've done is rename default.asp to index.asp, making their link 'dead' so to speak.