OMG. This issue were driving me crazy.
If you hacking around to solve this issue there is a really simple solution for that. You just have to change mods-enabled/suphp.conf and add the following lines.
AddType application/x-httpd-php .php .php3 .php4 .php5
You can check the complete file suphp.conf here
You can also do what this guy did http://www.howtoforge.com/forums/archive/index.php/t-55157.html He comment out those lines, however, I make no idea what are the security issues about this.
AddType application/x-httpd-suphp .php .php3 .php4 .php5 .phtml