Were you on a CO codeshare or a standard Amtrak fare? They give points differently.
As for the Coach/Business thing, on an Acela train, Business class IS coach. There is no coach on the train, and all Amtrak trains are 2 class setups.
If you are traveling on an Amtrak ticket and give you OP number, you get miles as you expected.
If you were traveling on a CO codeshare ticket, there is a lesser mileage accrual - like what you got. In the case of Amtrak you always lose by purchasing tickets from CO.
All of this is listed at
http://www.continental.com/web/en-US...er/amtrak.aspx