@Rose-A If you add one more step in "manually adding part" of your original post so that initial Invoice Payment is deposited to 12000 Undeposited Funds account all will work.
Receive Payment
...
Select the invoice
Select "12000 Undeposited Funds under" Deposit To
Hit Save and close
This way Bank deposit will work.
Hope this will help someone going forward...
Thanks,
R
