For some reason, when I tell Presenter to Publish, it thinks it's publishing, but it doesn't do it right. If Zip package is checked, nothing shows up at all. If I do not check that box, then it produces the data folders, but no index.htm file, or any of the SCORM files.
I have it set to publish in SCORM 2.1 with the settings shown here:
I was not able to repro this issue on my system. Are you seeing this issue with any particular file?? I made presentation with Question and Answer slides and did same settings as you mentioned, but everything worked fine for me. Can you try with new project?