If ballots had serial numbers and when you voted your name was tied to the serial number, and you got a carbon copy of your ballot after voting you could go online and check to see if your vote was changed or not. As long as there is no way for third parties to be allowed to cross reference the serial numbers with voter names (to keep the ballot secret to avoid reprisals against voters) this would eliminate double run and/or changed ballots. It would also require a cheater to tie ballots to names (so dead people voting would be easily caught and they couldn't just stuff anonymous ballots in the ballot boxes).

If multiple ballots with the same serial number showed up you could be contacted and then your carbon copy scanned to "correct" the vote cast (and the extra vote(s) thrown out).