The way I understood it Camcalc uses trig to allow for the angular offest of where it is cutting as well as the vertical and the cuts are all tangent to the profile as shown in green. Rod (Tangler) who wrote it is a member here so if he does not see your post why not PM him
At 39deg the cut will not be directly above the axis of rotation so will not be at 90deg to your black line
Scroll down to the second illustration of the latest version and you will see the blue (cut) lines are all tangent to the cam . The right angle formed by the angle of the vertical angle of the cam and the horizontal cut does not intersect on the cam profile as you have it shown on your first image but cuts it as your second images outer line
https://www.dropbox.com/home?preview=cam+with+draw.xlsYour ball nose cutter may be the problem as it may not be getting moved sideways enough to produce the profile which is based on using a flat ended cutter that will move either side of the axis. If using a ball nose cutter you will nee dto calculate Y movements as well as Camcalc's Z movements assuming X is the cut direction
If you look down the Camcalc heights it should show more than 0.208 for 39degrees