I'm pretty sure they don't count all links - let's say we have some really old web directory, that became a super farm link. Well, they won't penalize you for having a link there, because it was something natural to do back then (maybe even encouraged by Google, cus it's easier to crawl web when you have these hubs full of sites) but now they simply de-index these site or simply don't count them, because they have no relevancy.
But in these topic Im talking about cases like this - almost two months ago I built (okay, bought, but don't tell nobody) a do follow link from a rather good site and the article/text/link was indexed in day or two, but it's been added to GMWT only during these past few days.