Retained earnings not including capital loss

Turbo Tax Desktop for Business auto-calcs the retained earnings without subtracting out the net capital loss for the year.  Even though I manually enter the corrected retained earnings, when it gets to Retained Earnings Reconciliation Summary, it says there is a difference from the Tax Return figure and the Books figure.  If I say I'll review later and move on to the Balance Sheet, it is using the auto-calc figure instead of what I entered, so that is off too.  How do you get it to actually use the correct numbers instead of its calculation that doesn't include net capital loss?