When I check for backlinks for my site Google Webmaster tools says that I have a big fat zero!! But when I do the same for my blog it shows a much healthier 135 links. This is despite the fact that I started both around the same time and many of the backlinks for my blog are the same as for my website! Any ideas anyone?
It just takes time. It says the same thing for my blogs, and I know for a fact I have lots of links. Google isn't perfect.