This is interesting. I agree it is most consistent with Gox not having enough USD. It costs about 3% to convert to USD at retail in Japan.
The fee is 5% plus some, so it appears there is also an international wire transfer involved, with the various fees along the way.
After their USD losses perhaps they are running a fractional reserve in USD. The real solution here would be for them to actually explain what is going on.
I think it is public knowledge that $5 million was confiscated from Mt.Gox customer funds. Considering that it is a Japanese company that does not likely have such a sum of their own, excess funds, in foreign currency, this resulted in a deficit and fractional reserve in customers' accounts. It is almost certainly the root cause of this bank run.
Now,
the right way to do it (paragraph III.2 - - Special situations). If all firms operated this way, the pressure of unlawful seizures would be directly on the aggressor (USGov), and there would be no bank run possible.