I have seen something similar, however I have noticed a pattern
Whenever this happens, the user has completed, then immediately gone back into the SCORM. I haven't pulled out the magnifying glass on the logs yet, but I suspect they complete the scorm, and it doesn't have the tick next to it so they go back in to see what is happening. This sets them back to a zero score, however by that time the CRON (or somehting) has triggered the activity completion. (I noted that activity completion comes AFTER their second go straight into the module.
Can you check your logs and see if this is the case?
Cheers
Peter