I really didn't understand why he couldn't help me either, by calling the agent center (correct term?) or some kind of support, but it was clear he didn't want to do anything involving those tickets since it appeared that the first agent messed it up and therefore showing that I owed full price for the new tickets (difference would have been $1004 since they are now high bucket and purchased them at lowest bucket). He gave me a little piece of paper with AMTRAK's 800 number on it and said I should call and tell them about my inconvienence (which he still claimed he couldn't help). So I called and waited forever for customer service and finally got a hold of an agent that said he didn't understand my situation. He finally understand that my first re-route (outgoing) was messed up which was why the ticket agent wouldn't take my old tickets in exchange for no additional monies and noted that my return had now also been canceled and that they had already reassigned us to the Cap Ltd coming back. I said "Really, because that train is showing sold out and my current reservation does not reflect that change when you pull it up online." He said we had been switched to the same day Cap Ltd and he would fix everything for me but it would take a while. I asked him to please send me an email with the updated itenerary and he said he would and encouraged me to not print the tickets until the morning of our departure in case there were further changes. He said to "relax, I'll make sure it all gets taken care of" but never once offered me any compensation or credit for the inconvience of a one hour one way drive and back for naught.
I never did receive an email with our new itenerary and online reservation stilled showed Card but the adjustment had been made to reflect an even exchange when I return the old tickets. So, before I head back to the station to exchange tickets, I thought I should call to make sure everything is in fact taken care of and guess what? They still had me coming back on the Card and the same day Cap Ltd was sold out so they couldn't put me on that. So, basically, the fellow in customer service was as useless as the two prior agents had been. I finally got a good agent who fixed EVERYTHING while I was on hold and then immediately sent the email with everything correct. She handled it very professionally and understood the situation the first time I tried to explain the long, convoluted story. Kudos to her.
So now I will leave on my trip next week and see how the rest of it goes. I will probably contact customer service when I get back to explain the lack of followthrough and the mistakes made with my reservations but thought I would wait in case there was anything else to add to it. I am hoping not and am not expecting anything.
The plus side is that an additional day for our Chicago connection means a hotel bed and shower in between two nights in coach instead of two straight nights in coach and we are going to go watch the Red Sox beat the White Sox