IIS performance issue - very slow (w/ PHP)

I have a performance issue, and I'm guessing it is IIS but I could be wrong. I am not an IIS pro so I was hoping someone here could help me out or point me in the right direction.

Basically the problem is this: I have designed a web-app in PHP that reads large-ish XML files (300k each, usually 4 files), processes them then spits out the data in them onto the screen. It was all working ideally under WinXP (old server) but when re-formatting the server and installing Server 2k3 the application has been shot for speed.

In the past, reading 2 XML files would take around 0.7s and reading 4 XML files about 1.4s, however reading 4 XML files now takes 13-14s. Interestingly if I read only 2 XML files the time taken is about the same as before, 0.7s.

I've tried a few things including running the PHP as a CGI module as well as the ISAPI extension, changing output buffering settings and changing the size of the chunks of XML files read at a time through PHP.

Does anyone know what might be going on to cause this strange performance issue

I'd be looking at bad php code or incorrect permission settings. IIS6 and PHP work together well. IIS would have nothing to do with your php code reading and processing a xml file, that would be done in the php executable, not IIS.