Well, I am plagued by these pop-ups also, however I HAVE figured out an IP correlation for them.

When one of my connections drops and Limewire goes looking for a replacement, these popup boxes are showing up with the same IP addresses as some of the ultrapeers that Limewire is trying to connect to. If you stare at your connections tab you can catch it, although it's quick.

What I thought might be happening was that the IP I was trying to connect to was behind a solid firewall, requiring a login to connect or something similar, and those users hadn't disabled ultrapeer connections?

Either way, it still doesn't help me keep from crashing or rebuffing those requests automagically. :/

And yes, in UNIX files beginning with "." are hidden system files.