just got the second MACLO in GOD, one in Shadow of the Wickerman.
I don't have a single duplicate stack on Runes/Shards/EvoRunes/EvoShard and no stack is full.
81 souls total
122 Toons
127 out of 170 Talismans

Until yesterday i had several duplicates with quite some 99ers and over 100 souls for several days - not a single MACLO.
It seems that it's not the stacks that causes this.