I have an erroneous banklink count from a site, to one of my sites, stated in WMT. The link count from that site, according to WMT, exceeds 1,600. Yet, when I delve into the WMT statistics on that particular site, only 2 backlinks show up for that site. The site is reputable in nature. I've noticed that I've lost ranking for that effected page for normal keywords where I have ranked. I know, in theory, I shouldn't lose ranking from an external site pointing to me, but it appears that this "excessive link count" emanating from one site may be causing this problem, even though this link count is entirely wrong.
What gives with WMT's new super-duper back-end tools ? Anyone else see anything funky like this, with these undesirable results ?