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Does it really matter? Utilizing software to count the votes is ripe for mischief. And the first rule of mischief is: "if it is possible to perform, with a low likelyhood of getting caught, it will happen somewhere".

You need to first go read "Reflections on Trusting Trust [win.tue.nl]". Then consider the authors of the software running on the "counting machines". If they followed Ken Thompson's concept from "Reflections on Trusting Trust [win.tue.nl]" all the paper trails from the machines certifying what software versions are running on them would "check out", yet the machines could still contain code that, as it tallies the votes, watches the margins and slowly changes random votes from R to D (or from D to R) in such a way as to effect the final count.

Unless the local poll workers do a hand count to verify, they will be none the wiser that when they dropped a stack of 10000 ballots that were 4000 R's and 6000 D's that the machine counted them as 5500 R's and 4500 D's). They just get a final number (5500 R 4500 D) and report it, even though it is a complete falsehood.

Which is why all the ballots should be counted by hand, with monitors watching from all candidates to verify no funny business. But doing that would not let the entertainment cartel (CNN/MSNBC/FOXNews) broadcast their entertainment shows, so that wont happen.

Next best would be random hand counts of stacks that went through the machine, without the software on the machine knowing this batch is going to be manually hand counted (remember VW's diesel-gate, where the software detected when it was being "tested" and adjusted itself to compensate and pass the test).

So reports of software miss-counting -- you should believe this to be true unless proven by a hand count otherwise, no matter which party benefited from the software miss-counting. It is way to easy to do in software, either purposefully (see Ken Thompson above) or simply by creating buggy software.