In the Histogram window make sure the black clipping slider is all the way to the left and not clipping any shadow detail. Also, goto File>Setup and be sure to check the "enhanced shadow detail" checkbox. This checkbox is only for high dynamic range positives and shouldn't be used for negative scanning. Finally, makes sure Flexcolor's color management settings are coordinated with Photoshop's and that your display is properly calibrated. Keep an eye on the numbers. Flexcolor should be excellent for this task.