If your customer complains about a situation that when he tried browsing to a page that is mapped to ASP.NET ISAPI filter he get page 404 and there is no IIS log for that entry and even more you get connection_dropped message in the HTTPERR (Error logging in HTTP API) than I suggest to you as a first action to remove the ISAPI extension from IIS restart the computer and register it again (All manually).
We had the same issue and NOTHING worked other than this method (not even reinstalling IIS).
I could not find any reference to this on Microsoft site BUT when we opened a premier ticket to solve the issue that was the first step (there goes more than 5 hours of wasted time)
Hope this will save you lots of hours!!!