Although not quite Search Engine Optimization, but related in a way. I have used Google Webmaster Tools for many months to keep a check on my sites. Ensuring no errors in sitemaps and watching the quantity of inbound links build up was quite satisfying. The tools have however changed recently. One of my sites that had over 700 inbound links now only shows as 200 or so and my other site that had 400 inbound links shows as only 1!! I know these inbound links still exist, so anyone any ideas what Google are playing at?
It might be overlooking the backlinks with rel="nofollow" and some less important links, however you can try out submitting a structured sitemap showing all links from one page.
I've since found a couple of conversations on the Google forums about this issue. It seems I am not the only one losing links to the new system and there is no fix in sight. My site which has the fewest links and I was building up, I have manually checked the existence of my inbound links and they definitely do not have the nofollow tag.
I thought I would try the old link:webaddress to see the difference and Google again reports no links to the site, although Yahoo gives me pages of them?
Interestingly enough though, there must be some inbound links of a reasonable quality as the Page Ranking has risen from 1 to 2!!
Also those are just sample links which are generally shown in webmaster tools, to check your inbound links in more detail you should use different tools.
As the Google Webmaster Tools have been updated recently, it might be possible that there are some changes in the Tools due to which there are some in changes in the results. If you are not sure that the results are correct you can use some other tools available to check the backlinks. One such tool is Yahoo Site explorer.
Google changes its strategy of indexing and ranking to avoid spamming and black hat Search Engine Optimization which is widely used by many of the websites to achieve good rank...just update the website according to the new rules and regulations declared by google and your website will again acquire the same ranking and position....