After a bunch of research I was able to solve my issue. For some reason mcrypt only had it’s mcrypt.ini file in the /etc/php5/conf.d folder. The file also needs to be in the /etc/php5/apache2/conf.d and /etc/php5/cli/conf.d folders. I simply copied the file to those 2 directories and restarted apache and then the active directory options worked again. If anybody else in ubuntu has this problem check those directories for the mcrypt.ini file.