If there is a difference, the means the sum of the transactions you've marked as cleared does not add up to the ending balance entered.
The formula is:
Beginning Balance + sum of activity = Ending Balance.
...or, with more detail:
Beginning Balance + sum of deposits - sum of payments = Ending Balance.
So, if the beginning balance matches your statement, and if you entered the correct ending balance from the statement, then if there is a difference, either the sum of deposits or the sum or payments must be different than what actually cleared the bank for the statement.
