And here's the feedback I received on your comments:
1. No external links, internal links, or sitemap links use http://gadgetguy.com.au
so this would not be an issue.
2. Internal Duplication is a very recent issue; however again the
Sitemap and all the Index and Section home pages use the latest links
which are being crawled, so this should not be a significant issue.
Duplication does not explain why neither page would be indexed, or why
deeper indexing other than Homepage and Section Home is not occuring.
3. Commas in URLs we will investigate.
4. Long/keyword stuffed URLs. Have edited to fix issues of length and
keyword stuffing.
5. Invalid Code - mmm... I very much doubt this is an issue. The
DocType is used by the browser to work out how to interpret the HTML
at render time. Google has no interest in this, so I see no reason how
this could cause a problem.
6. We don't have hidden content. The DIV layer being hidden is an
empty formatting control.
7. Google is happy the sitemap is valid. We also validated the sitemap
independantly before submitting. However, as this is dynamically
generated there could be new content or very old content in it that is
appearing for the first time; nonetheless if there was a problem the
Google Webmaster report would report it - and there are no issues
showing at the moment.