Difference in Sage Bank Account and Actual Bank account

Ive been having an issue for a while now but im not sure how to amend.  My Sage Account balance and Actual bank account are about 2k difference.  I do my reconciliation each month and apart from 13p difference, its all fine.  I do however have duplicates that I just leave as I don't know how to get rid of them.  I have asked before but its so confusing that I just ignore it. Is this why there is a difference do you think??