If you completed a 2011 filing on a 2011 form (for example), the "Prior Year Filing" box would not need to be checked. However, this box needs to be checked if you are completing a 1988-2010 year filing which is filed on the current year's form (the 2014 form at this time). This box ONLY appears on the draft Form 5500 and will not appear on the final PDF version of the form.
If you received a "Not Accepted" status due to the following DOL edit check:
--> Error: Form Year in the Filing Header is not valid for the plan year, which is determined by the Plan Year Begin date in the Filing Header.
You will need to "Amend" your filing to review your draft Form 5500 to determine if you will need to check or un-check this box.