It sounds like you don't have index.php in the list of Default Documents. Add index.php to the list as shown below. You can also do this through the IIS settings for Default Document.
<defaultDocument>
<files>
<clear />
<add value="index.php" />
<add value="index.asp" />
<add value="Default.asp" />
<add value="Default.htm" />
<add value="index.htm" />
<add value="index.html" />
<add value="iisstart.htm" />
<add value="default.aspx" />
</files>
</defaultDocument>