[Zak]

I ran into the same problem on a version 4.11 with the sku box having to be checked after returning no results. I finally figured out that you have to edit the product search form to include the sku input.

Open skin1/customer/search.tpl and find:

<FORM method="POST" action="search.php" name="productsearchform">
<INPUT type="hidden" name="simple_search" value="Y">
<INPUT type="hidden" name="mode" value="search">
<INPUT type="hidden" name="posted_data[by_title]" value="Y">
<INPUT type="hidden" name="posted_data[by_shortdescr]" value="Y">
<INPUT type="hidden" name="posted_data[by_fulldescr]" value="Y">

And add:
<INPUT type="hidden" name="posted_data[by_productcode]" value="Y">

Hope this helps...