I think grand juries are designed to indict suspects on preliminary evidence. If an indictment results, a warrant for arrest is issued. Congress would not be involved in this matter if a US Attorney is involved (i.e., Dept. of Justice =/= Legislature).
OK. But do you agree that "there must be a pending suit in a civil matter or charges filed in a criminal matter before a subpoena can be issued" is completely incorrect?
Subpoenas often come
before someone is charged with a crime.
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To tie this back to the thread, it's certainly possible that the US sent Mt. Gox a subpoena because they were investigating possible wrongdoing, and when the attorney working for Mt. Gox looked into things to try to respond, they came to the realization of "oh shit, Gox doesn't actually have any money!" The investigation leading to the subpoena may or may not have been related to the lack of money, in such a (hypothetical) scenario.
Again, the only part that is really hard to imagine is that these problems were caused solely by transaction malleability and that no one at Gox knew about them until very recently. Surely if Gox really did lose hundreds of thousands of BTC due to transaction malleability, someone on the inside knew about it and/or was involved in cooking the books.