All of the state-funded routes are profitable (or at least break-even) from Amtrak's perspective.
No, Amtrak still runs a small loss on all but the VA routes.
I think that is mainly because they just could not convince anyone that what they were claiming the cost is based on the mystery cost allocation algorithm that they seem to be unable to explain even to themselves sometimes, was actually believable. So they were stuck negotiating a mutually acceptable price. In short they basically swallowed the bitter pill of reallocating those extra allocations somewhere else, but just in case, they still call them allocations to the operations that will never pay for them. I don't quite understand the logic of that, but c'est la vie.
I have heard usually reliable hearsay that Pennsylvania steadfastly refused to accept Amtrak's demands on the Pennsylvanian until Amtrak caved. Same is true of the course that the negotiations with New York took. It apparently came to a point where New York was quite ready to walk away and have Amtrak shut down operations and then try to explain to Congress why they did so. Amtrak at that point decided that desecration was the better part of valor and backed down. This one was particularly ironical since 10 or 12 years back it is Boardman sitting on the New York side of the table, that was decking it out with Gunn regarding the Turboliners.
So whether it is a loss or not is still open to question. Who knows? Just because you throw a dart at a board and allocate a cost does not necessarily make it a real cost. It does however make it easier to remove that cost from something else. This is a favorite game that is played by large corporations when they write down losses. If they decide to do so for whatever reason they will load up everything including the kitchen sink that they can pass under the scrutiny of the SEC. Since stuff written down cleans out the books and allows things to look much much better, until the next time.