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I propose a more reasonable rationale for the increase between the Dallas office proposed fine and the actual fine levied. From the article:
Typically, once the FAA officially proposes a civil penalty, the airline and the agency negotiate the amount down, a process that can take years.
Dallas FAA suggests a $2M fine. Washington FAA office <redacted> knows AA will fight it and get it lowered so they raise it to make a statement knowing these were serious issues and the fines should reflect that, so they propose a $25M fine. Sometime down the line AA pays a fine around the original amount proposed by Dallas office. The end. <redacted>