What does the fading selection color mean? In the picture you can see that the last vertex selected on the edge loop is somewhat separated by a color change from the rest of the selection. What does this mean?
There are actually two vertices in the exact same position there, which can be seen as you noted by the differences in edge shading. 

I would box select where the manipulator (the blue, green, red arrows) are and either hit alt-m to merge  or hit W > Remove doubles.