It's generally a good practice to open a separate bank account for estate business, to avoid mixing estate funds and personal funds. Keeps things transparent and in good order and, sometimes importantly, makes it easy to demonstrate that they have been kept in good order if anybody is so rude as to question that at any point in the future. (And you can open this account and put funds into it before obtaining the tax clearance certificate.)
Once you have the clearance cert you can then reimburse yourself out of that account for properly incurred estate expenses that you have personally discharged.
I can't say if this is a factor in the delay here, but you might find the bank less anxious about transferring the money if they were transferring it into an estate account.