Hi,Maybe I can help. What is the actual problem you're seeing?
I'm having trouble interpreting the image you provided. Can you explain how the image demonstrates the problem?
First of all I would like to say that is not the author of this applet; I've found it on this forum. So I don't know how MPR is implemented in this applet, but I've tried to follow the steps from your webpage and it seems like the penetration dir is slightly inaccurate for this case.
The red and green polygons are the colliding objects and the blue polygon is their Minkowski difference (MD). The red and green large points are the closest features in the polygones returned by the algorithm, coresponding to the yellow point on the MD.
You can see that the distance from the origin to the yellow point on the MD is not the shortest (I've marked it with a red line). The shortest distance from the origin to the MD (that is the penetration dir) is marked with a green line. I've marked the brown point as the correct point, both on the MD and the two polytopes drawing.
I'll try to make more captures from the algorithm steps for better understanding.