With recounts everything gets scrutinized by eyeball. From signatures to hanging chads... Anything to disqualify your opponents votes and anything to count votes for yourself... The rule ought to be that if the machine won't count it, it doesn't count. If the voter (I was going to say citizen... But we know that isn't true...) isn't bright enough to properly mark his/her vote too bad.
That explains it, but there should NOT be TWO ways of counting votes! They should CHECK the FIRST VOTES that CAREFULLY!