Most likely you are not displaying the sidebar when the costumizer is active which prevents the costumizer from detecting its existence on the page.
The costumizer detects the sidebar by hooking on various sidebar related hooks that are supposed to be triggered when the page is generated. If for some reason your sidebar display code do not trigger the hooks the costumizer will not know it is there even if the actual content is being displayed. This can happen for example if you cache your sidebar and instead of calling dynamic_display you just output the sidebar.