since you're not new to running sites I'm guessing you already know this, but just in case: if you do have both a www and non-www version of your domain did you set a 'preferred domain' in webmaster tools? If not, google reads both as two diff sites, and links to one version won't count towards the other
Assuming yes, I do a lot of reading about how to use webmaster tools/analytics and I've stumbled across a few discussions about links not showing up in gwt. It seemed to be a glitch in the program where the data exists but just wasn't appearing. I just googled (haha) trying to find one of them and found this:
http://www.seroundtable.com/google-w...unt-16315.html. There's lots of articles though if you search for 'google webmaster tools missing links', I just grabbed one of em.
it seems like most people impacted recognized the problem when their link counts drastically dropped, but since your site is relatively new it could be that the glitch was occurring as you gathered links (meaning they never showed up in gwt in the first place)?
It seemed people were talking about the glitch in early Feb and it's now apparently been fixed....maybe a few weeks isn't enough time for google to add links that never appeared in the first place due to the glitch? How your site ranks would probably be a good indicator of whether it's just missing info that is actually being tracked by google or a deeper problem.