Definately do not mail in the actual ticket stub. If you do that and they loose it, you will no longer have any proof that you took the trip. What you want to do is to make a clear photocopy of the ticket stub and mail that copy in, along with a brief letter giving your name and account number. But by no means give up the original ticket stub.

As for the online missing points form, I find that it can be hit or miss. The fact that your ticket came from a source other than Amtrak may very well be causing part of the problem.