I agree with Daniel, there is ample evidence of tampering with election results in the US system.
As for ballot papers going missing, all papers are accounted for, scrutineers, of all political persuasions, observe the initial count, which is done by the same people who mark your name off the roll, then cross checked by the electoral office, electoral rolls are also cross checked to ensure no one has voted more than once.
All ballot papers are signed by the electoral clerks before being handed out and the numbers tallied at the count. I worked on the polling booths for many years, I can't recall there ever being more than a couple of votes (in tens of thousands) not accounted for, often the missing papers were found in the garbage where disgruntled voters had thrown them.
Usually the numbers of papers tallied exactly.
This article, in Rolling Stone magazine, on the role of electronic voting in the 2004 US election, is well worth reading.