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“The FCC document references the 18 Fox owned stations and says nothing about the 200+ affiliate stations.”

Im fact the FCC mentions the affiliates several times. One example: “Therefore, we find FOX responsible for broadcasting the Promotional Segment containing the EAS Tones on 18 of its owned-and-operated broadcast stations, transmitting the Promotional Segment to 190 of its network-affiliated television broadcast stations, and causing the transmission of the Promotional Segment on Fox Sports Radio and the Fox Sports on XM channel.”

> Are those stations culpable if they also broadcast Fox produced content that was in violation of EAS rules?

Station licensees are responsible for the content they broadcast. In this case at least the FCC went after the content source, which is itself also a licensee.