Patience might be needed: From the Amtrak site terms and conditions:
4. Once Choice Privileges points have been requested, points will automatically be transferred to the member's Choice Privileges account and deducted from the member's Amtrak Guest Rewards account. Please allow 60 days for points to transfer or show up on account.
BTW, there is a thread in the Amtrak forum on the Amtrak-Choice conversion
http://www.flyertalk.com/forum/showthread.php?t=746558