I have noticed an issue with Totara 2.5 relating to completion.
In the past, if you edited completion settings for a course after users already had some data, it would warn you about it and allow you to "unlock criteria and delete existing completion data". After editing and running cron, it would reprocess everything and create the completion records again (in the mdl_course_completion_crit_compl table).
However, with the latest version, it no longer recreates those records, and thus in the Completion report, none of the modules will show as complete.
Possibly a side-effect of the "instance course and program completion"?
To reproduce, setup completion on a resource in a course, and set it as required for course completion. View the resource with a user, then view the Course Completion report. The user should have a checkmark.
Now, edit completion for the course, and choose to delete existing data. Save completion and run cron. The user will no longer have a checkmark in the Course Completion report.