Yes, unfortunately you are in the same boat. When you originally filed with the refund transfer option, the bank account number that was passed to the IRS was the number for the temporary account that was going to be opened in your name to receive the refund. Even though your tax return was delayed and you had to pay separately, that is still the only bank information the IRS has for you, unless you went on the IRS website over the summer and corrected your bank information.
Thanks and sorry for the weird grammar. I was limited to very few words in the question. Word around the campfire is that if you CHOSE to pay separately you have to file the stimulus on this year's return. I did pay separately, but was forced to due to delayed processing, eventhough I chose to have fees taken out during filing.