JS_Harris - 5:54 am on Mar 18, 2010 (gmt 0)
What you're describing is very normal, lets consider where your links are for a moment.
Mostly they are low-quality links from blogs, free directories, forums, and social networking sites, but a few are better-quality links from independent websites.
Now lets consider what happens to those pages over a three month period, they fall deeper and deeper into a sites link structure or archive (takes more clicks to get to them) and so the internal link value passed to those pages diminishes... eventually taking them off the GWT radar.
I've heard some people refer to 2nd tier link building campaigns, if you've heard that saying too it means building a link campaign to boost the pages that link to yours. I don't have the patience to do this because I spend my time working on my own content but if you prefer link building to writing articles you can always build a solid foundation for the pages that support yours too. :-)