Thanks Jeremy.  That makes sense.  But, I'm not sure if that how this appliance is working.

Weird thing is that when I do

php -i

I get

Configuration File (php.ini) Path => /etc/php5/cli
Loaded Configuration File => /etc/php5/cli/php.ini
Scan this dir for additional .ini files => /etc/php5/cli/conf.d
Additional .ini files parsed => /etc/php5/cli/conf.d/curl.ini,
/etc/php5/cli/conf.d/gd.ini,
/etc/php5/cli/conf.d/imap.ini,
/etc/php5/cli/conf.d/mcrypt.ini,
/etc/php5/cli/conf.d/mysql.ini,
/etc/php5/cli/conf.d/mysqli.ini,
/etc/php5/cli/conf.d/pdo.ini,
/etc/php5/cli/conf.d/pdo_mysql.ini,
/etc/php5/cli/conf.d/xcache.ini

So since this came from the command line, it probably should show ../cli/php.ini etc.

But when I've made the changes to /etc/php5/apache2/php.ini and do the service apache2 restart, the changes aren't taken and SugarCRM continues to show errors.  I didn't notice this until a few days ago when SugarCRM kept on giving me an error that it didn't know the date.timezone. I put the date-timezone="America/Toronto"  in /etc/php5/apache2/php.ini a few weeks ago.  So I couldn't figure out why it wasn't working.  Then I found this php -i command and found there were two of these ini files.

Now that I put the date.timezone into /etc/php5/cli/php.ini there is no SugarCRM appliance error.

Strange....