Once that data is in SCORM Engine, you can use the SCORMEngineManager to retrieve data from the registration object. Here is a great article about how to use the SCORMEngineManager to retrieve runtime data for reporting.
This all being said, is your course SCORM 1.2 or SCORM 2004? I wonder if the issue isn't that it is not being stored, but if it is using too many characters in suspend data. SCORM 1.2 has a pretty limited number of characters to work with, specifically 4096, so if the course goes over that amount _and_ it uses suspend data to bookmark, you may run into issues here.
The good news is that if this is the issue, we do have a package property in SCORM Engine that will allow you to increase the maximum suspend data. You can manipulate that maximum suspend data size through either the package property editor in your SCORM Engine implementation, if you expose it, or by hitting the SCORMPackageProperties table directly and changing the value of the suspend_data_max_length to "64000" which is the maximum for SCORM 2004. This will normally get you around this issue.
If this creates more questions, please feel free to create a ticket by emailing me directly at firstname.lastname@example.org