The E-Commerce module is changing a lot, therefore the templates of most, it not all themes are not matching the ecommerce code any more to 100%. Try using the ecommerce templates of the pages where the sub-groups should be shown which come with the ecommerce version you're using instead of the ones included in your theme.

In most cases that fixed such issues for me.

Not different themes, but replace the specific template (the one where you have the problem) in the theme you use with that same template taken from the ecommerce module code.

Or in other words:

1) Identify the template used by the page where the problem shows.
2) Find that same template (same name) in the ecommerce module.
3) Copy that template from the ecommerce module over that same template in your theme (replacing that template)

Most of the theme's look is defined in the CSS of the theme (which you keep) so the look should be still matching your theme anyway.

That worked, thanks. The layout is screwed up, but the links are showing. I think I just need to update the CSS file to include a few things that the theme didn't account for. I'm using the Plain theme, so I know it's fairly old.