Which of the 3 PHP methods do you give to your customers? Are you sing php as module or fastcgi or cgi wrapper (what exactly is the difference between those two anyways ? :) )
On our non virtualmin servers we use suphp which is not available in virtualmin (eventually for a good reason) and i feel that mod_php has some security issues on a shared webhosting server. So for now we go with fastcgi.
Feel free to let me know why you decided on the php you use.