I'm not located in NYC, but I was able to use transit checks to purchase one-way tickets on Amtrak in addition to round-trip and 10-trip tickets. Maybe you could try another agent?

My employer contracts out the transit benefit fulfillment to Accor Services (also called Commuter Check Direct). They offer a Mastercard that you load your transit benefits onto. It says "Debit" on the card but you use it like a credit card. I find this very flexible since I no longer have to deal with an agent to purchase tickets with transit checks. If you have this option, I highly recommend it!