Hi Kevin,
Looking at Default.aspx.vb, I see that The dnncore.js is added to the page at line 214, as:
Page.ClientScript.RegisterClientScriptInclude("dnncore", ...)
This inserts the script at the very beginning of the page form.
Looking at Default.aspx, I see that a <noscript> tag is indeed included, but it is BEFORE the form.
You might try moving this tag into the form element. However, I'm not sure if 508 compliance requires a <NOSCRIPT></NOSCRIPT> after EVERY script include, or just the last one. If it's the latter, you'll be forced to modify Default.aspx.vb and manually insert these tags after every script registration.
Hope this points you in the right direction!
Brandon