Hi dides... 

Can you give a little more detail?  Are these fees that were changed by the bank and actually showed up as transactions in your Bank Account?  In theory you could not have Reconciled if you did not have a $0 Balance every month.

My guess is these Fees that went to the CC Processor and came out of the sales processed before it reached your Bank Acct.  So there should not be any kind of entry in your Bank Acct that was not actually a Transaction in that Acct. 

You should have an Expense Account for Credit Card Processing Fees.  If it doesn't already exist, just to to your Chart of Accounts and Create it.