This is because there is a difference in timing on block and on hit. On hit, Sub-Zero will be done with B12~Aura more quickly than he will on block. This means that on hit, your timing is right B12~Aura, B12 will come out properly. On block, it takes a bit longer for Sub-Zero to be done with B12~Aura. As such, your second B12 will not come out because the timing is difference. The reason as to why this exist is likely because it makes it easier to confirm that your opponent has blocked your attack.
A way to see that this is true is to pick Kung Lao and do 11212 on hit and on block. On block it is easier to do, because it takes a bit longer for Lao to be done with 11 on block, giving you more time to input the 212.