Confusing site: results - Google seems to ignore my canonical redirect

[nmjudy]

I'm confused. I have a 301 redirect setup for my example.com to redirect to www.example.com. I also have www.example.com set as the preferred domain in Google webmaster tools.

However, when I use the Google site command I get totally different results for
site:example.com
site:www.example.com

The most confusing part is the non-www domain is showing a couple hundred more pages.

Is there something else I should be checking?

[edited by: tedster at 2:16 am (utc) on Sep. 15, 2008]
[edit reason] switrch to example.com - it can never be owned [/edit]

[tedster]

You're right, that is confusing. The first thing I'd do is verify that the server is really sending a 301 status. I'd especially check on the urls that are showing up without the "www".

Check the server headers live with a browser, not just by looking at the server configuration.

[nmjudy]

I recently implemented a site-side redirect from /directory/index.html to /directory/ on a 7000+ site. See discussion on setup:
[webmasterworld.com...]
[webmasterworld.com...]

I've submitted a sitemap dropping all the index.html pages and pointing to the directory itself. Google Webmaster tools is currently showing both versions on alot of pages. I'm assuming that they're still in the process of figuring out that index.html doesn't exist?

Using the Firefox Live Headers plugin, this is what I see in the redirect. It looks ok to me. Do you see anything that looks broken? (I just ran a find/replace to change out the domain and directory names)

Note: the TTL is short - I'm getting ready to move over to a new server. I thought the shorter TTL would force Googlebot to recheck pages quicker?:
http://example.com/directory1/directory2/directory3/index.html

GET /directory1/directory2/directory3/index.html HTTP/1.1
Host: example.com
User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.9.0.1) Gecko/2008070208 Firefox/3.0.1
Accept: text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8
Accept-Language: en-us,en;q=0.5
Accept-Encoding: gzip,deflate
Accept-Charset: ISO-8859-1,utf-8;q=0.7,*;q=0.7
Keep-Alive: 300
Connection: keep-alive

HTTP/1.x 301 Moved Permanently
Date: Mon, 15 Sep 2008 13:43:50 GMT
Server: Apache/1.3.39 (Unix) PHP/4.4.4 mod_auth_passthrough/1.8 mod_log_bytes/1.2 mod_gzip/1.3.26.1a mod_bwlimited/1.4 FrontPage/5.0.2.2635 mod_ssl/2.8.30 OpenSSL/0.9.7a
Location: http://www.example.com/directory1/directory2/directory3/
Connection: close
Transfer-Encoding: chunked
Content-Type: text/html; charset=iso-8859-1
----------------------------------------------------------
http://www.example.com/directory1/directory2/directory3/

GET /directory1/directory2/directory3/ HTTP/1.1
Host: www.example.com
User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.9.0.1) Gecko/2008070208 Firefox/3.0.1
Accept: text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8
Accept-Language: en-us,en;q=0.5
Accept-Encoding: gzip,deflate
Accept-Charset: ISO-8859-1,utf-8;q=0.7,*;q=0.7
Keep-Alive: 300
Connection: keep-alive

HTTP/1.x 200 OK
Date: Mon, 15 Sep 2008 13:43:51 GMT
Server: Apache/1.3.39 (Unix) PHP/4.4.4 mod_auth_passthrough/1.8 mod_log_bytes/1.2 mod_gzip/1.3.26.1a mod_bwlimited/1.4 FrontPage/5.0.2.2635 mod_ssl/2.8.30 OpenSSL/0.9.7a
Connection: close
Transfer-Encoding: chunked
Content-Type: text/html

[tedster]

Ah, now I see. You made the canonical fixes quite recently. It can take a while for Google to sort all that out. Their huge database is not like an instanteous desktop application - lots of things are going on, especially when they check through 301 redirects for trust issues. I've seen large sites take quite a few months before all the debris disappeared from the live SERPs.

In short, give it more time.