I edited the above reply but missed the edit window. Here is the corrected reply:
Thanks! I should have been more clear on what I meant by 'root directory:' they are sitting in Portals/0. That's where the test site was pulling them from until the upgrade to the latest DNN version. I'm not a developer; I'm more of a front end person, though I can do a little back end stuff. So are they in the right place?
On the live site home page, http://www.ikasystems.com/Home.aspx, I see this code for those two images:
<link rel='SHORTCUT ICON' href='/Portals/0/favicon.ico' type='image/x-icon' />
div id="header">
<div id="logo">
<a id="dnn_dnnHEADER_dnnLOGO_hypLogo" title="ikaSystems" href="http://www.ikasystems.com/Home.aspx"><img id="dnn_dnnHEADER_dnnLOGO_imgLogo" src="/Portals/0/ikaSystems.png" alt="ikaSystems" style="border-width:0px;" /></a>
</div>
There is no reference to the favicon in the test site home page source. And the header div is missing a reference to the logo file.
<div id="header">
<div id="logo">
<a id="dnn_dnnHEADER_dnnLOGO_hypLogo" title="ikaSystems" href="http://www2.ikasystems-test.com/Home.aspx"></a>
</div>
I don't know how to add the references to the test site pages, though, since the code is automatically generated.