TheOptimizationIdiot - 11:36 pm on Apr 2, 2013 (gmt 0)
I would guess you removed too many.
As we know from the recent help the BBC got from Google an "unnatural link notice" can mean links to one or many pages, rather "all or most links" to a site in general. ("All or most links" to a site is how I would think most people would interpret the BS notice, but that's not necessarily what it means.)
It probably doesn't help you much now except to know it might be better to ignore the FUD they spew via WMT and do your own thing in the future if you can't figure out exactly WTF the notice (or any notice they send) is talking about.