I have had a similar problem which commenced during Nov/2010, but I had not upgraded or changed anything that I am aware of during that time. For the months of Nov2010, Dec2010 and Jan2011, my blog only shows one or two posts, but there have been many more. Oct2010 displays fine in the Tabbed sidebar Archives.
I did upgrade about 2 weeks ago to 3.x and the latest Suffusion theme to see if that would fix it - clean up some of the code or convert badly saved posts or something.
I created another 3.x MU site and imported the exported posts in xml and the problem still persists on a totally new site, with no other content or random directory issues.
I looked at some other posts - http://wordpress.org/support/topic/moved-blog-to-root-directory-archives-stopped-working?replies=5 to see if this was relevant, and still, as far as I can tell it is not.
If I switch themes, (eg. default 2010) and the archives for those months are fully populated. If I switch back to suffusion, only some of the posts appear. I have tried the above method - "Template Tag Shortcodes" plugin, then insert a short code for [wp_get_archives] on a page and this looked promising, but when you click on these months, it is missing the exact same posts for each of the last 3 months?
I am relying upon the Suffusion" Date-based Archive Page settings to display the archives in the tabbed sidebar.
Is there anything else I could check?