Not for THAT account, but do you have another account? Then you could just transfer those 1000 baht to your immigration account in the morning, before even leaving home. Skip the CDM machine, just update your passbook.
Alternatively: If you have an ATM card for another account, you could also use that card to deposit money into your immigration account at a CDM. The card is only used to identify you the depositor, you can deposit money into accounts the card is not linked to (even other people's accounts at other banks).