However, a web page that includes the same file with the mssql_connect call still works fine, and now it makes sense that I see mssql is still enabled in phpinfo.

The apache version of the php.ini file is different to the cli version. Make sure you are looking at the right one.

On debian I have two separate directories for each config - /etc/php5/apache2/ and /etc/php5/cli/

Try this:

php -i  | grep 'php.ini'

from the command line to work out which php.ini to look at.

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