so when you manually create IT0009 where you able to see the IBAN number in PA0009 table?
please can you run the below reports for only 1 EE then see what happens
RPUFIXDS
RPUPAV00
once you have run the report sucessfuly then update IT0009 IBAn then check then PA0009 it may or may not work
but please let me know the out come of this
all the below post is related to IBAN but none of them is related to your issue
IBAN number issue in IT0009 | SCN