It sounds to me like the site where the links are coming from could be at fault.
Do you know if they have made any changes recently? It is very easy for bad coding to produce thousands of pages that the site owners aren't even aware of (speaking from past experiences here). When you look at some of the pages where the links are coming from, do they look like nonsense pages?
It's a little difficult to tell exactly what is at fault without actually looking in more detail, but as this is just one site, it shouldn't cause you any issues - if it were an attack of some kind, then you would be seeing links from different domains, rather than just the one.
-Andy


