To answer my own question, this problem was caused by the deprecated function "get_course_students" now found in /lib/deprecatedlib.php. It's query was formatted in such a way as to return all students who hadn't logged into Moodle yet.
The bug is documented here, as is the fix:
http://tracker.moodle.org/browse/MDL-7592
This bug was fixed in the Moodle 1.7.1 source code.
Journal (plugin)
Journal Shows All Students, Not Just Class Roster
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