I have a brand new website that was indexed within five days. Not bad. only problem is...I have more than a few backlinks from "doFollow" forums to my index page. When I do a Link:www.mydomain.com - it shows no backlink. Also...one more thing. When I do a site:www.mydomain.com - it doesn't show up as indexed. It only shows up indexed when I do a site:mydomain.com - anyone have any ideas what's going on?
Don't rely on google to check backlinks. Throw it in a backlink analyzer like http://www.linkvoodoo.com to see your links.
Try other backlinks checker. Here you have 29 backlink checker with dofollow and nofollow, anchored text, etc. http://atniz.com/2009/03/20/29-backlink-checker-and-link-analyzer-sites/
google takes a while to update backlinks, sometimes as much as couple of months. if you are searching for backlinks for a new site, then try yahoo explorer which works lot faster. regarding inner pages not being found, looks like google didn;t index your inner pages. and also look like you submitted or build backlinks without www for which you are facing this issue. only use one uniform URL, with or without www. if you are using both and want to stick with one, you can use 301 redireect which will solve the issue
wait for few weeks to get the google back link status.. the same www. is the problem for me too.. thats not a big problem...
Sign up for GOOGLE WEBMASTER TOOLS at Google.com (its free). Google provides the most comprehensive list of Links --- for example-- my site has 6,800 links at Yahoo Site Explorer, but you can only SEE 1,000 (about 14% of total links, and they omit most of the good ones) At GWT (Google Webmaster Tools) -- I am able to see 2,415 links (250% more than Yahoo shows me).