This document might explain some things:
http://de.scribd.com/doc/209050732/MtGox-Situation-Crisis-Strategy-Draft At this point 744,408 BTC are missing due to malleability-related theft which went unnoticed for several years.
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Switch off the MtGox exchange temporarily (1 month) while announcing a restructuring and re-branding
They must have had exactly no checking/accounting practices in place, if they failed to notice thousands of BTC missing for years.