Google admitted to a bug causing some webmasters to show a deflated number of links within the Google Webmaster Tools link report.
There were several threads at Google Webmaster Help dating back to August 5th with complaints. In a few, Susan Moskwa updated these webmasters that there was a limited bug effecting some webmasters.
Hey folks, we did have an issue that caused some users' backlinks numbers to drop earlier this month. It should now be resolved. Thanks for letting us know about your experiences -- it helped us to track down the problem.
Webmasters have confirmed the links are not being reported accurately in Webmaster Tools.
Forum discussion at Google Webmaster Help.