When you upload the file through EBS,
1) the bank account number appearing in the upload file (say in case of MT940 file it appears in the tag 25) is validated with the data entered in table T012K which is the FBZP table.
2) If entry found then it tries to find the entry in table T028B which is the EBS table.
In your case, please check the 2nd validation. Check if your file have leading zeros in the file, then it should contain the same both the tables.
If still not cleared, then please give us the test data of the entries maintained in both the above tables and also the account number appearing in the upload file.