Sometimes LMS doesn't count slides

On both Cornerstone and Exceed LMS's, and whether the course was created in-house in Storyline or by a vendor using another software, sometimes (like 4% of cases), the course won't be marked as complete/passed when the user completes the course. 

This only really seems to happen in courses where the completion is set by slide counting, so when I create courses in-house, I always just use a Trigger or quiz score to mark complete.

But I'm wondering if this is a common thing that "just happens sometimes" or if there's a fix people have discovered? Both LMS support desks, along with a third party consultant, were no help. They universally say it's the course's fault, not the LMS's.

My LMS tracks the amount of time people spend in a course. Sometimes it will show someone has spent less than a minute on a course that they actually completed. Sometimes it will say they've spent hours and hours (sometimes over 24 hours) on a course that they actually completed. Sometimes it will say they haven't even launched the course, even though they've actually completed it. It's like something just gets "stuck" in the communication between the e-learning module and the LMS.

Could it be an issue with user bandwidth? Some of my users are on pretty spotty WiFi (though not all). I don't think it's a browser issue, because IE and Chrome have similar results. It's not Flash or HTML5. It's been happening for years, and there are similar results for both of those formats.

Anyway, have others experienced this? Any tips?

UPDATE: I've only ever used SCORM 1.2. SCORM 2004 and Tin Can have compatibility issues with my LMS.