That is hardly proof of anything. You don't post anything else about your site. We don't know the history of the site, we don't know the content, we don't know if you did any other link building.
My thoughts would be that Google was considering moving you into an authority position for your keywords, and their system did a review of where your links came from, and realized it was all completely duplicate content on every link page. It is like putting 5000 links on Malware sites and hoping for a good boost from google. It isn't necessarily the AMOUNT of links, but rather what kind of links, and where they are placed.
Also, 3 links from same site? Why? 1 site, 1 link. Don't need anything else. If you were doing it for direct clicks, you would have been better off using unique content on just a few article submissions.
Another thing to consider when it comes to getting "thousands of links fast" is blogrolls and recent comments widgets. Sometimes I drop a link in a comment, and that comment moves to the recent comments widget on EVERY PAGE of the site. This can mean 500-5000 links from 1 site in just a few seconds. Does every website that gets put on a blogroll or recent comments widget get "sandboxed"? NO.