Chelsea midfielder Lampard won his appeal on Tuesday against his sending-off in Saturday's Premier League victory at West Ham, when he and Luis Boa Morte clashed. He will now not serve a three-match ban.
Boro were furious when their appeal against Jeremie Aliadiere's red card at Liverpool the previous weekend was dismissed as "frivolous", costing the striker an additional one-game ban.
Aliadiere was dismissed after slapping Javier Mascherano on the cheek.
Gibson said in the Daily Star: "I am trying hard to make sense of it all. It astonishes me. The whole system is flawed.
"It was the right decision by the FA to take way Lampard's dismissal as TV evidence showed there was nothing violent.
"But how can the FA say that was any different to that involving Aliadiere?"
An FA spokesman told The Times: "The FA treats all cases on their merits.
"We would refute any suggestion that one club is being treated differently to another."