In version 2.6, we fixed this issue.
That means for some users who inadvertently had all these checkboxes unchecked and didn’t know it, updating gives the appearance of your SEO meta entry fields disappearing. If this happens, don’t be alarmed. No data is missing. Simply go to wp-admin->All in One SEO Pack->General Settings and scroll down to SEO for Custom Post Types and enable this setting then check the boxes you’d like under SEO on only these post types (Posts and pages are checked by default on new installs.)
Users also report not seeing the Display Settings section, this is because that section will not be populated with options until you enable SEO for Custom Post Types. If your Display Settings section is empty then make sure you enable SEO for Custom Post Types.