@alabamaseo and @Stevie D,
Google Webmaster Tools has just crawled and now the "Duplicate Title Tags" count has increased to 2,256
These are typical links, one with .html and one without.
Using Health->Fetch as Google Bot for the one without the .html extension shows:
Fetch as Google
This is how Googlebot fetched the page.
Date: Tuesday, April 23, 2013 at 9:45:49 AM PDT
Googlebot Type: Web
Download Time (in milliseconds): 267
HTTP/1.1 301 Moved Permanently
Date: Tue, 23 Apr 2013 16:45:50 GMT
Expires: Thu, 19 Nov 1981 08:52:00 GMT
Cache-Control: no-store, no-cache, must-revalidate, post-check=0, pre-check=0
Set-Cookie: PHPSESSID=70b448b533d272edff1fb8df8537bb44; path=/
What more can I do? The canonical link is correct and "HTTP/1.1 301 Moved Permanently" is set. Is Google reporting incorrectly showing the "Duplicate title tags"?
The correct link show "HTTP/1.1 200 OK" and the canonical link is correct.