Dear Chris,
It sounds to me as though you've come across a bug in the IMS Enterprise enrolment plugin. It seems quite a complex plugin in that it can handle account (and course) creation, in addition to user enrolment. A quick search of moodle.org and the Moodle Tracker suggests that it is not used much. I couldn't find any report of the problem you describe, so please feel free to create a tracker issue for it yourself.