Just an update on the whole ticket buying, train travel experience. We took this trip about 10 days ago and the e-tickets worked exactly as they should have--great!
As for the refunds, I certainly didn't have the experience that LHR/MEL/Europe FF had. I sent two e-mails to IRCTC right away when I noticed all the redundant charges, and they did a few of the refunds within a week or so. The rest of the refunds are only coming through now, several months after the initial booking, and in fact after the travel was completed! Since I had taken the initiative to call Amex right away and tell them about the overcharges, I never did have to pay them, but the process was not at all seamless or quick.
I did enjoy my ride. That train is showing some serious wear and tear though--when I took it about five years ago, the cars looked fresh and new, but no longer. Still, the meal service was fabulous as ever (providing hours of entertainment!)