Often this occurs when new Account/Checkbook ID's are set up, if the Bank Account number is blank in the CM00100 field (for Bank Account).  To check this please go to Cards – Financial – CheckBook ID and fill the account number that would match the account number inside the bank file. Be sure to include any leading zeros so that the Bank Account number and Checkbook Account number match.   The account number will show as xxxx behind the 03,xxxxxxx (search the bank file by using CTRL F and 03).
Another cause can be due to missing transactions in the imported file.  In the bank file, verify if there are any "16,xxx" lines in the import.  If there they are missing, this indicates no transactions are in the file to be imported.
Also be sure to verify the Reconcile dates are the same in both Microsoft Dynamics GP and the bank file to be imported.