I get the silly smart stack problem as well. mostly happens with smelted ores, so, metals, mostly with iron and silver for me, and rock. i have a full smart stack of sedimentary rock, but 3 of the blobs are only about 50 instead of 99, and if i take them out of the stack, then put back into the stack, they do not combine and overflow into the next spot, they just fill in the empty spot i just took them out of.
and the metals mostly happen when i have the number 18 or 27. dont know why. i silver in a smart stack, with other metals, and the iron is in 79, and 99, and 10, wont combine. silver in 18 and 27. will not combine.