I have submitted four websites in google webmaster.But when i watch "links to your site" in search traffic of websites in google webmaster,two of mine website's links are not shown.I think i have submitted my all websites 2 years back and my all sites are shown their back links.It is started from few days (only for 2 websites) and all other thing is fine.
Maybe those links were not crawled by google bots. Are those links visible on other backlinks checker tools.
Case 1: You might have setup Google webmaster tool on non-www version and you have backlinks on www-version. Case 2. You might have setup webmaster on www-version and you have backlinks on non-www version. Solution: Can you redirect to non-www to www or you can do reverse as well. If you don't want to do this setup two webmaster account(one for www-version and another non-www version). I prefer 301 redirect.
Webmaster tools link data is inaccurate and incomplete. Don't rely on it. I have one site with over 30k links to it with other link checking tools and Google shows zero! It's really not a good source of links.