I don't have an exact answer but you could check to see if a custom template was accidentally applied to the autonav or go back in under edit mode and double check to make sure your setting are what you want (for example "display all" under the third option in the autonav edit window.).

If this doesn't work - delete the block, exit edit mode and publish changes, re-enter edit mode and add the autonav block again with the proper settings for drop down menu.

Did you mark any pages as "exclude from nav"? Sometimes there are problems because the system only excludes that one page you set that attribute on, but continues to include all of its sub-pages.
Another option is if your theme's CSS just isn't set up properly to display the correct dropdown menu using the html structure that autonav outputs.