Specifically on the Kenya/Uganda situation. Kenya's 2 pixels are dead in the middle of its area, and the rest of its area is in the surrounding cells, but unfortunately none of it occupies more than half the are in that cell. Uganda on the other hand gets lucky, it shares its cells with other countries yet is aligned such that it occupies more than half of each cell.
The best example I can think of at the moment would be Chile. All of its cells would likely not occupy the whole cell, yet it would be counted for it since it occupies more than half. Let's say it gets 20 pixels, then it might actually only have, say, 10-11 full pixels worth of area, but it gets 20 pixels due to the half-area rule.
Uhm... but in the little image above the quiz, I can see the Africa map with all the borders and this is a great help!
Firstly, a grid was overlayed on top of the usual Africa map (with non-Africa countries removed). Then the next step was to remove any squares within the grid that had at least 50% of the square covered by the usual map. So, for most squares inland, it had almost 100% land, thus was kept, but some coastal squares had very little or perhaps no land at all and were removed. Secondly, each square was then analysed manually to work out which country's land occupied the most area in the square itself. Most squares were easy to do since a single country occupied 80-90% of the land, but some became more challenging to analyse as the amount of area was quite similar between two countries.
Hopefully this helps to explain a little better. As always feel free to ask more questions and I'll gladly answer them :)
I'm only just discovering it now for some reason, and I absolutely love it! Really great work again Stewart.