I'm not sure I can answer your actual question (if someone out there can, I'd be interested too...) but I can tell you NOT to be obsessed with monitoring your links. They'll grow if you are consistent and keep at it - and your rankings will improve. And then all of a sudden you'll realize that your links are growing more exponentially and you'll have nothing to worry about anymore. Just keep at it -- pages come, pages go, some sites keep your link, some drop it, the search engines update their stuff all the time. Don't worry so much.
I am not too sure why. But, I saw a similar "sudden overnight drop" on MSN's BLs too. It's a month old site and last week it was showing around 400 BLs on MSN. Then, overnight they dropped to around 250 and then to 220 or so. Anyway, I spend at least an hour (or more) each day working on BLs on this site and since last week they have been crawling back and are back at around 250 now and growing. Why did this happen? Well, nobody can answer that question with certainty. But, I think that they might have set-up a filter that filters out site-wide links down to 5 or 10 (say). I think that MSN was picking up all of my links from my signature from this forum, perhaps 150 posts or more as BLs. They might have set-up a filter that filters these down and only counts a certain maximum number of links from each domain. At the time when I was showing 400 links, I was pretty certain that I only had around 200 or so. So, IMO that's all there is to it. Do you have a large number of links (or site-wide links) to your site from the same URL??
I can't say for sure if MSN does have this filter. This is just the theory that seemed to make the most sense to me and seemed to fit in well with my site's situation at the time. I believe that most other SEs grab all BLs but don't display them all. Ex: If your site has 100 BLs (say) and you check your BLs through Altavista, it might only show you 30-40 links and not display all (multiple ones that are from the same URL). Whereas MSN seems to ignore these "extra BLs" completely.