This might be caused because you have tried to move your custom meta box to some place and WordPress respects the user’s ordering/positioning of these boxes. You can do as gmazzap has told because this will create a new user with blank preferences.
Or you can login to your database, find DBPREFIX_usermeta (DBPREFIX is your database prefix) and find related database entries. In my case:
You can see meta-box-order_PLUGINNAME (where it is your plugin’s name) and screen_layout_PLUGINNAME. When I removed these entries, the problem was gone.