Skin Modifier base

Hi. I'm having some issues with this. Posted before but received no answer. Clear interface. Ctrl A, edit mode, shift w and bring it down to a single point. Extrude up. Add skin, add mirror. Move mirror up. Extrude point for arm. Discover that the upper point separates from itself and is attached to the bottom at the main point. What is going on? Do I have a setting that is wrong?