@Aaron
I ran into the same issue with trunk r73999, it seems to have worked before somewhat with 0.5.2, at least I could see FeaturedProducts .
Checking the ProductGroup.ss in ecommerce trunk r73999 there is no ChildProducts etc. mentioned anymore, just FeaturedProducts and NonFeaturedProducts.
The Product group setting at the products and the Child Groups setting at the product group define together if a product is shown in the NonFeaturedProducts or not.
Thus all the code of the current ecommerce templates, at least for ProductGroup.ss, needs to get adapted to that change, if you wanna see your products.
Based on that I assume that what you see and describe is not so much an error on your side but more likely the first steps of the changes visible in trunk now.
Here's how it's handled in ProductGroup.ss in trunk, may be that can help you:
<% if FeaturedProducts %>
<h3 class="categoryTitle"><% _t("FEATURED","Featured Products") %></h3>
<div id="FeaturedProducts" class="category">
<div class="resultsBar typography">
<p class="resultsShowing">Showing <span class="firstProductIndex">1</span> to <span class="lastProductIndex">$FeaturedProducts.Count</span> of <span class="productsTotal">$FeaturedProducts.Count</span> products</p>
</div>
<div class="clear"><!-- --></div>
<ul class="productList">
<% control FeaturedProducts %>
<% include ProductGroupItem %>
<% end_control %>
</ul>
<div class="clear"><!-- --></div>
</div>
<% end_if %>
<% if NonFeaturedProducts %>
<h3 class="categoryTitle"><% _t("OTHER","Other Products") %></h3>
<div id="NonFeaturedProducts" class="category">
<div class="resultsBar typography">
<p class="resultsShowing">Showing <span class="firstProductIndex">1</span> to <span class="lastProductIndex">$NonFeaturedProducts.Count</span> of <span class="productsTotal">$NonFeaturedProducts.Count</span> products</p>
</div>
<div class="clear"><!-- --></div>
<ul class="productList">
<% control NonFeaturedProducts %>
<% include ProductGroupItem %>
<% end_control %>
</ul>
<div class="clear"><!-- --></div>
</div>
<% end_if %>