Only one file had a different SCORM settings (since it had a quiz). I had not changed the SCO IDs.
My "Multi-SCO SCORM Package" is grayed out so what I did was—publish each file into its own folder without zipping it. file1.htm went to file2/file2.htm, which at the end of the project went to ../file3/file3.htm, etc. Then I packaged the entire thing and uploaded it.
Do I need the multi-SCO SCORM package?
I have gone in with my current settings and changed the SCOs but it's still not working. Will my file structure allow bookmarking?