i was just in google webmasters tools. at the top there was a link "We're changing! Check out our new look!" so i clicked it. for a second, i was like big deal, new look. then i clicked external links. one of my sites that had 4313 links in the old tool only had 797 in the new tool. i compared them and i cannot find a reason why some of the backlinks are not there. it has nothing to do with nofollow/dofollow because there are nofollow backilnks in the new tool. hopefully it is just that the new tool is just a sample.
Thanks for info! I've checked it and found that there are less backlinks in the new tool - 15%-20% less then in old tool. But there are 10 times more inner pages with backlinks then it was in old tool.