It depends on which city is putting you "over the top" on your tech research and how many beakers it produces. The beakers from each city are applied to only one tech, so if you've got a city producing 50 beakers and only need 10 more for your current tech, 40 beakers from that city are wasted. However, any cities processed after that one will go to your next tech. I am guessing you have a SSC in the first city you put down, and it is producing the bulk of your beakers. It is probably this city that is throwing you "over the top" each tech so any extra beakers produced in you SSC are lost. Early in the game, you don't have a dominant SSC, so almost any city is equally likely to be the one that puts you over the top, and when that happens, you get the beakers from the remaining cities applied to your next tech.