I have a workflow that was created in production, we made changes to the workflow in our test environment then exported from test to production. It is now creating a duplicate in the manual start of the drop down options on the files. There are workflows running on current documents in the library and we don't want to terminate those by deleting the prior version but for all new workflows we want them to run on the updated workflow.
Screen shot attached.
If you try both of the options, does one give you an error? If so, you'll need to use SPD to remove the "broken" menu item from the list.
Another way I've solved this issue (and proactively stopped it from happening) is by un-checking the "Start Manually" option from the existing workflow's Workflow Settings, publishing the workflow to remove the menu item entirely, and then immediately importing/publishing the new version with "Start Manually" checked. This should leave you with one menu item.