I am not sure how the U.S Attorney decides what cases they will take quite frankly. I imagine it would also depend on the method that the theft occurred. Frankly, I lowered the figure. In the five cases I have had, the fugure actually was around $500,000 which is the cut off after which the jail sentence significantly increases.
The amount in controversy that you mention is a civil claim threshhold. It has no application in criminal law where the critical issue is the use of the mails or interstate actions to make it Federal.Incidentally, just about anything that is put in a bank involves use of the mail since it is sent by mail from the first repository to a second bank or a main repository.