Function name conf_init() in civicrm.config.php collides with function in Drupal bootstrap.inc

When I upgraded to CiviCRM 2.1.4 and Drupal 6.8, I found that I could no longer run /cron.php. The error was the the require statements for CiviCRM include files were failing. After way too much research, I put include('../sites/all/modules/civicrm/civicrm.config.php') in the cron.php page and ran it manually and got an error about the conf_init being duplicated.

function conf_init is defined on line 236 of includes/bootstrap.inc in Drupal, and on line 37 of sites/all/modules/civicrm/civicrm.config.php.

My website root is different from my drupal installation (/ vs /drupal). This may be part of the problem here.