One possibility - and this is based on Moodle 2.7, not sure if it was the same in 2.5 but assume it probably didn't change that much.
check mdl_course_completion_crit_compl.
As an example - having worked on something similar to reset individual users in a course to allow them to take it again - our purpose is for recurring (yearly, every 3rd yet, etc) staff training - I found I had to remove information from the following tables for a course that contained a just single SCORM module and a certificate.
{certificate_issues}
{course_completion_crit_compl}
{course_completions} (not actually deleted anything here, just changed timestarted to = and timecompleted to NULL)
{grade_grades}
{scorm_scoes_track}
if anything was left in one of those tables, I noticed the same thing that when the cron ran it would reset a lot of the information that was removed.
One other thing, you mention mdl_quiz_attempts, but what about the final mark in mdl_quiz, did you remove that as well?
Kevin