I was trying to book a trip we have taken several times in the past--all successful btw--which used the EB connecting to the CL (now just under 3 hour connection time), and Amtrak will not allow this booking. The customer service person said 2 hours and 45 minutes is not sufficient time given the EB's "expected" performance parameters in 2015. Well, I guess that sums up how confident Amtrak is that the EB's recent decent timekeeping will last--not!!!! Bummer.
The only connection offered is via the LSL and then a NE regional train, which adds almost another 1/2 day to my travel planning, not worth the effort. I can't imagine an airline saying that 3 hours was not sufficient connection time between flights. :-(