Accessing IIS Web apps with Nestscape

I have had two Web applications that worked great in Internet Explorer, but timed out in Netscape. I fixed the first one by installing the software into the IIS root. I tried this with the second and it didn’t work. It is a web search engine and I have already rewritten it and contacted their tech support (no help at all). I have a strong suspicion this is an IIS problem, possibly a problem with redirection. Any ideas why this is happening?