I'd be pretty nervous about enabling manual completion because I've never actually seen it work properly.
I would do two things...check the settings for the scorm to make sure it isn't fighting completion because of completed vs. passed for some (I never use those requirements...I set a grade and make sure they can attain it--either through a quiz in the score or through a variable on the last page (captivate and storyline might do it differently...). Also check that there isn't a completion restriton (must read/view something) that isn't a completion criteria setting (not required for the course but required for the activity) that most people completed but not the ones who aren't getting checks.
Now for two...and this sounds scary. Unlock completion criteria for the activity and save. It will as if you are really sure...say yes. It will clear completion and grades temporarily. Actual attempts and scores will still be there. This may end up resetting the date of completion for the course, but it doesn't sound like is an issue.
After doing this, you'll have to wait a bit for the sync...but it usually works for me. Other options? I will sometimes reset the course completion criteria, too. Occasionally grade to pass rears it's interfering head, you could check it (grades->setup->edit settings for the activity (might have to click show more). I don't think this has ever interfered w/score before, but there's a first time for everything.