The amount of yeast in each bottle doesn't really matter. However if the priming sugar was not well dissolved, it is possible you got more sugar in some bottles than others, and that would make a huge difference. Changing over to sugar cubes is helpful in ensuring a consistent amount of sugar per bottle. However the best way to add priming sugar is to measure how much you need for an entire batch, then boil 2 cups water and dissolve all the sugar in the hot boiled water, let that cool for a few minutes, and then add the fully dissolved sugar solution into your bottling bucket (or perhaps Mr. Beer in the earlier cases). It needs to be completely dissolved in order for this to work -- if any sugar sinks to the bottom of the bottling bucket then you will have big problems. But if you use enough boiled water to ensure that it's not too thick and syrupy and fully dissolves, and you mix it into the bottling bucket pretty well, then you will not have any problems with consistent carbonation. It will never settle out over time as long as it's not still crystalized and not syrupy. The couple of hours it takes to bottle will not make any difference. If you left the beer sitting for a whole day then you might have issues, but for just a few hours, no big deal.
I use about 5/8 cup cane sugar for 5 gallons, which is equal to 2 tablespoons per gallon. If you use corn sugar (which is NOT necessary) then you need to use a little more, 3/4 cup for 5 gallons. Add the sugar to boiled water in bulk, and then you won't have to mess around with sugar cubes. Sugar cubes will work just fine as you have seen, but they can be a little more of a pain and less consistent.