I think an underlying reason for the commuter agencies abandoning Amtrak as the contract operator is the threat made by David Gunn back in 2002 to shutdown all of Amtrak, including the fully funded contract commuter operations, unless increased funding for the was provided by Congress. This despite the fact that the agencies pay all Amtrak costs (plus profit).
While effective at the time as leverage to obtain the increased funding, that threat infuriated the commuter agencies and, I think, ended the days when Amtrak was considered a contractor of choice for such operations. Not wanting to be a pawn in the annual Amtrak funding battle, the agencies began to look long and hard at what other options are available and, surprise, other options are out there.
Despite what Amtrak likes to think, they are not the only people who can run passenger trains in this country. Mr. Gunn probably thought that the 2002 threats would galvanized the political support of the commuter agencies behind Amtrak. Instead, the agencies are going to Plan B and telling Amtrak to take its problems elsewhere.