If I define a page for use as a shell section and set it for each section (header, footer, right, left) for a custom shell it only renders for the Header and Footer, not the sides. Nothing funky, just a simple portlet on a page.
You may have to define a fixed width for the left/rightnav. First try setting a pixel width (like “200px”) for the section’s column(s) (in the layout properties of the column in the page editor); if that doesn’t work you can try setting a width as the css style (like “width:200px;”) of the section’s row(s); and if that doesn’t work, try setting a pixel width on one of the elements in your portlet.