When editing a form each question has its own save button, it sounds like maybe you are not clicking that but instead clicking the Save button at the bottom of the page which does not save the question but only saves the number of pages for the form.
I suggest compare the functionality of Form Wizard Pro on our demo site vs your own site. It is working properly there and I have no explanation why it would work differently on your site. I cannot produce the problem you describe. You might also check the error log for any errors that look related to Form Wizard.