I have a similar problem and have isolated it done further but with no success so far.
I am developing a hosted site using php with the following: linux/Apache 1.3.12/php 4.0.1pl2 as a module/mysql 3.23.47. phpinfo() and all my web pages and php scripts work fine with IE6.0/Netscape 4.73 and Opera 6.0.
I develop localy and upload using the following W2K/Apache 1.3.20/php 4.1.1 as a module/mysql 3.23.47. I just changed php from cgi to a module. Before I made the change all my pages worked fine with all three browsers(except for PNG files on netscape which I am going to change to JPEGs.) and phpinfo() worked fine.
I unistalled php cgi and reinstalled php as a module today. All my pages work fine and phpinfo() works fine on Netscape and Opera but has the download problem with IE6. The ScriptAlias and Action directive make no difference. With or without them I get the download problem in IE6.
My relevant lines in my local httpd.conf are as follows:
LoadModule php4_module modules/php4apache.dll
AddModule mod_php4.c
AddType application/x-httpd-php .php
Since I can use phpinfo() in Netscape or Opera and my pages work fine its not a real problem for me but I would like to find out what's going on here.