This happens when flow sheet dates are opened out of order. The first moment that a flow sheet DOS is open, is the moment that everything will flow forward from the previous DOS. So, for example, if the 2nd DOS is open in the flow sheet, and then you go back and add, edit, etc functions in the 1st DOS, those changes won't flow to the 2nd DOS. The best way to see if a DOS for a FS has been opened, is to click the Visit drop-down. Any dates with a check-mark next to them have been opened.
To fix this issue, unmark all the fxns so that they are grayed out. Then right-click 'Delete Flow Sheet Visit' (this will take away the check-mark next to it in the drop-down). Then click the Visit drop-down, and select the date again. Now it will flow forward the info from the previous date, capturing all the latest info.