by Ken Task.
SCORM is typically part of core so when the site upgraded it should have upgraded the SCORM module along with all other core modules.
Did you get a separate prompt to upgrade the SCORM pllugin? Do you have any SCORM addon?
Also, the last thing and upgrade does is run through all default settings - doesn't change them (or shouldn't).
SCORM's could be large ... one could be uploading the zips to a file system repo which is outside of moodledata/filedir/ and either copying them to Moodle or using a symlink to the zips when setting them up in moodle. So how have you been uploading the SCORM's to your site?
Suggest turning on debugging ... all the way to developer level so we might be able to determine the cause.
'SoS', Ken