Does anybody ever run into a problem of backlinks from domains not appearing in your site links in google webmasters? I actually had backlinks appear from a replication site - but not the original one (forums that replicate on more than 1 domain)
Google is pretty good but some possible reasons could be:
1. Google has de-indexed some of these links for some reason,
2. Google has not crawled these pages recently,
3. You don't have a canonical URL. The link may be pointing to www version of your site and your default is without www (or vice versa)
Strange linking reports are also observed by a lot of people these days but they are some temporary issues actually. By clicking on the links and moving to the last page you would again find your accurate links counts. Maybe Google is trying to update its links reporting issue in a way to pick the incoming links faster than before.