Have you actually seen first hand the course page with the student logged in? And although I know you changed the docking, are you absolutely sure he hasn't docked it before and it is still docked?What if for a short while you allow user themes and he changes the theme - does that make a difference?
I think he did end up docking it without realizing. He sent me screenshots but I couldn't see the edge of the screen, so I couldn't see that he had done it.
I told him about the docking and now all is well.
On another note, though, it seems I can select No for "Allow user to dock this block" for Navigation and Settings, but not for other blocks, such as Messages, Recent Activity, Online Users etc. (The option is not available.) Any reason for this?