The FileMaker Server install uses IIS and sets up PHP (or uses an already installed version). But it does not specifically do something about ASP. The only thing I could think of is when in IIS it is setting up the directory for fmi/iwp that it overwrote something also used by ASP. But there is nothing on this in the FileMaker knowledge base. So I am sort of not believing this is FileMaker's issue, but eagerly listening to see if anyone else has observed this phenomena. If even one more person sees this problem, I will believe there is a problem with the FileMaker installer. Lets see if anyone else can confirm this behavior.
Also... are you implementing new services using ASP? I thought it was a dying technology just being bandaided for old web sites made in it for the IE6 days. Then again, I'm not a web develoer and may not have any idea what I am really talking about.