I am using the desktop Turbo Tax and it doesn't ask to fill in Box 6 when entering data from the 1098. Instead, points are entered in a subsequent mortgage screen. When entering the 1098 info for each mortgage, Turbo Tax asks if it is 'the latest 1098'. The answer is No for the first 1098 and Yes for the second 1098. Are you making these selections?
Try entering the points on each 1098 first. Then only on 'the latest 1098' if that doesn't work.
