The IgnoreIsActive flag allows you to choose which profiles to sync. By default, only the active profiles in a content database get sync'ed. An active profile is one of a user who has contributed something to the site. If you want to sync all users in the site, you can choose to trigger the execution of the sync job via STSADM with the IgnoreIsActive flag set to 1, and it will sync every profile.
You can investigate what profiles are marked as active, by looking in the UserInfo table of a specific content database. The tp_IsActive field will have a 1 for active, 0 for inactive.