When using the feature "restrict start points to preferred regions" it seems like simplify3d tries to find concave regions of the print to hide the seams in. This is a wonderful feature. The issue is it does not really look for concave regions, and instead looks for angles between triangles, and ignores concave regions where the angle between them is greater than 135 degrees. This means that if you are using fillets in your cad model (as is very commonly done in 3d printing) because the internal cocave fillet is made up of a bunch of triangles that each have angles greater than 135 degrees the seam will never be hid in those regions. The seam will only be hid in "sharp" concave corners. I think simplify3d should look for the most concave regions of the print to determine where to do seam hiding, not what seems to be a hard coding of the angle. On the simplify 3d page for V5.0 where they are advertising the better seam hiding the example part would not work if the designer placed fillets in the concave regions of the model.
Here is an example where the angle between triangles is 135 degrees, it hides the seam great(look at the retraction and wipe move):
Here is an example where the angle between triangles is 137 degrees, it does not hide the seam at all:
And this is where it decides to place the seam, on a convex region that is very visible: