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Hi Tarik, Unfortunately, no one tool can track all your links. Open Site Explorer is the best tool on the market (in my opinion) for backlink research, but Google Webmaster will almost always show you more. The problem with Webmaster tools is it often shows you "junk" links, links that pass no value, and it leaves out many of the links that count. It leaves a lot to be desired in terms of finding actionable insights into your incoming link profile. The advantages of Open Site Explorer are two-fold. 1. SEOmoz tends to show you the links that pass value, filtering out most of the "junk" that Google doesn't count anyway, and 2. SEOmoz attaches metrics to the URLs of the linking pages and domains (DomainAuthority, MozTrust, Etc) so you better understand the value of your backlinks and those of your competitors. That said, SEOmoz isn't the only game in town. Majestic does a fair job of reporting links, and you'll often find links there you can't find in other places. My tool of choice is SEOmoz, because of the accuracy of the Index and the associated metrics. In the end, you'll have to discover the solution that works best for you.

I would give it more time to see if your links are going to be indexed and focus on building a 'natural' link profile. Building 100+ links in a short space of time with a new site can be dangerous if they are low quality/spammy. My advice is to slow down and focus on quality links from a range of sources.