Let's start at the beginning:
During the "testing", why did the system deduct one vote from Raila and not all the others?
Not seeing anything. Are you missing some url?
Algorithm theory: In situation where 41,000 polling stations are rapidly and progressively releasing per-polling stations results - this provides a near perfect uniform random distribution that should reflect the final results at every given time. It doesn't matter if 1K are in or 30k are in - the final tally will be the same - because this is near perfect random sampling - there will small changes here and there because maybe NASA or Jubilee stronholds have slighlty better internet or less votes - so they are likely to marginally report their results earlier or later.
For example.
1)If good random sample of 41K - say the first 1000 polling stations randomly transmit their results from every corner - it should represent the final tally - 54% verus 45%.
2)If good random sample of 41k - say the next 10K polling station randomly transmit their results from every corner - it should represent the final tally -54% versus 45%
3)If whole set of 41k station all submit that information at ONCE - it should reflect 54% versus 45%.
In short this actually the basis of opinion polling - and this results vindicate IEBC.
You can compare and contrast with 2007 which was acknowledge by many to have been rigged for wild swings!