I was having a similar problem. PHP was working on my sites configured by virtualmin but not for phpmyadmin. PHPMyAdmin would not execute and the file was being downloaded by the browser. Everything I was reading was saying that libapache2-mod-php5 was not installed but I knew it was... so the thing to do was to purge it and reinstall.
sudo apt-get purge libapache2-mod-php5
sudo apt-get install libapache2-mod-php5
sudo apt-get purge phpmyadmin
sudo apt-get install phpmyadmin
sudo /etc/init.d/apache2 restart
