Shytown,
You say he had no idea that the ticket was in that sleve. What happened to that sleve? Did he throw it away? Or is it someplace that you can still get it? If you can recover that lost ticket, your life will be much easier and you'll get more of your money back. In fact, if you can find the ticket, you have up to 1 year to either refund it minus a 10% penalty or trade it in for either another ticket or a voucher, which will give you 100% of its value.
Without the ticket however, life is far less rosy. You'll have to follow the lost ticket procedures and that will require waiting and only getting about $94.50 back, as Amtrak will charge a $75 fee and a 10% penalty. If you request a voucher good for future travel, then you can avoid the 10% penalty, but not the $75 fee.
The ticket is considered cash by Amtrak, and therefore if lost it's like standing on the street corner handing out $10 bills. The agent did indeed follow Amtrak procedures, as outlined
here. Note: The form to report a lost ticket can be linked to from that page. But first, make sure that there is no chance of ever finding that ticket.