When storing eggs in a stack of 64, it only stores 16. To reproduce this, you will need hook up Quantum Storage Unit to a Refined Storage network, with a Exporter including 1 Stack Upgrade and 3 Speed Upgrades. I tested this with a regular Minecraft chest and it works fine. But it glitches out with a stack of eggs of 64.

QuantumStorage: 3.3.2
Refined Storage: 1.2.25
Minecraft: 1.10.2