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.

<Directory /usr/share/phpmyadmin>
AddType application/x-httpd-php .php .php3 .php4 .php5
suPHP_AddHandler application/x-httpd-php
suPHP_Engine off

You can check the complete file suphp.conf here

You can also do what this guy did 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
suPHP_AddHandler application/x-httpd-suphp