Consider the following chain of events.
Joe never bothers to request extensions for late filing of his tax return.
March, 2013: Joe does a rough draft of his 2012 taxes. He estimates that he overpaid his taxes by $12000 which he plans to carry forward to his 2013 taxes.
June, 2014: Joe finally files his 2012 tax return 14 months late. There is no 2012 penalty as he owes no tax. Joe credits his $12000 overpayment to his 2013 tax return.
July, 2014: Joe files his 2013 tax return which shows a $5000 over payment (after including the $12000 carry forward).
For 2013 payments, when is the $12000 carry forward from Joe's 2012 tax return considered paid to his 2013 account? Would Joe incur a late filing penalty because the $12000 wasn't "paid" until Joe actually filed his 2012 tax return?