This is just wild speculation now... ...but my best guess is their trading engine was so unstable that they ended up using one server to run a stripped-down cl

This is just wild speculation now... ...but my best guess is their trading engine was so unstable that they ended up using one server to run a stripped-down clearance house algorithm for executing the trades as quickly as feasible, and a separate system that was the "source of truth" for how many physical assets in bitcoin/yen/USD were actually in possession by the company. I'm guessing that there was absolutely nothing "atomic" about the system Marc Karpeles had built, their storage system was just an amalgam of disconnected, duct-taped databases living in different places, that were "kinda, sorta" in sync with each other, with lots of unpredictable, undefined behavior.