According to the filing, "Circuit City made extensive and good faith efforts to comply with this unprecedented regulation despite lack of notice or baseline for compliance." It also goes on to complain that errors were made by regulators in assessing the fines.
Assuming the company's claims are rejected by FCC officials, which seems very likely, the next logical step would be a lawsuit to have the rule invalidated in federal court. This wouldn't be completely unprecedented either. In 2005 a federal appeals court struck down the controversial broadcast flag, saying the FCC overstepped their authority by regulating how a signal could be used after being received by consumers.
Although this case doesn't deal with the signals themselves, it seems legitimate to question whether the FCC has any jurisdiction over retail labelling, an area of law typically associated with the Federal Trade Commision (FTC).