This is just a guess, but could it be that all those thousands of links came from forums/blogs and the like where pages get 'archived' and maybe the archived pages are below the required PR to show or maybe they just arent indexed yet ?
my numbers changed from 110.000 to 40.000 Of course there are sessions when they change from 70.000 to 200.000
Possibly a combination of hitting different datacenters, plus changes in supp pages. Google is always tweaking.
I had the same problem, when I first checked it listed all the sitewide links as separate links (i.e. if i have a sitewide link on site with 200 pages - it counted them as 200 links), but then it got "merged" and only counted domains. I assume its not that someone suddenly removed so many of your links, it's just that G recalculated them.
Google occasionally gets an upset tummy - spits all sorts out when it rumbles and then stabilises again. Who knows? .
i think it depend on how hard working the spider bot perform on your site. if they are lazy it will report the lower no. to the server. if it works hard, sure it will go to lots of your page and report all to server as well. so try feed them some food and they will come to crawl your site more often .