BenFox - 1:09 pm on Dec 23, 2010 (gmt 0)
It could be that your link checking tool just updated it's index - or that you're using two different tools which have different sizes of index. Also make sure that the settings are the same on both reports.
Check that your tool is set to external sites only. If it's counting internal links then *facepalm* and carry on.
It could eaisly be that one (or more) of the sites that link to you has duplicated the link on dynamic pages. Export your data to a spread sheet and get a count of the number of domains linking to you.
Try to figure out where the links are coming from. Is a scraper distributing your content across a network of spammy sites? Or are they all appearing as footer/blogroll links in low quality blogs?