I've just tried assigning users various different roles in the features demo course on demo.moodle.org (running Moodle 1.9.5+). Only users with the role of student appear in the course gradebook.
Ryan and MB, can you try reproducing your role problems on demo.moodle.org. If you are able to reliably reproduce the problem, please create an issue for it in the Moodle Tracker. (You'll need a tracker account in order to do so.)
Gradebook
Guests in Gradebook
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