We've had this same phenomenon, and documented the disparity between the usage at our router (running Gargoyle 1.4.7), at the modem (agrees with the router), and at our Status Meter (overstated). We would like to compare it to the hourly usage level on my.hughesnet.com, but we've had the "OpenID" error there for more than a year, even after multiple tickets about it.
Edit: I see now that sgoshe figured out that his phantom usage wasn't actually phantom. FWIW, our overstated usage only occurs when we have a heavy usage period. E.g., we actually use 500 MB in an hour, and the status meter goes down by 900 MB. This isn't a very chronic issue for us now, as we've slowed the data transfer rate on our router, and try to keep the actual hourly usage from peaking like that. Still, it's an unfair limitation that we need to observe until Hughes acknowledges and addresses the problem.