There is an option that can be select in the Auto Bank Reconciliation that ignores header rows:
From the Main Menu go to Auto Bank Rec Template.
Select the Template you are using by highlighting the line.
Select UPDATE.
Put a number of rows you need to ignore in the option 'No. of Header Rows (to ignore)'.
Select SAVE.
NB.
The system will ignore the number you put in of Rows, if you need this doing at the bottom of the Data there is an option for the Footer and this will do the same ignore the rows in that box.