I'm writinting because i experienced today a similar problem than "scottnsf".
I red with interest the answer from Lord of the Rings but unfortunately it didn't help.

First I have to say I'm using Limewire for 1 year now and it works perfectly well. I use it with a powerbook G4 1,25 Ghz/512MB ; under mac OSX 10.2.8 and I recently upgrade to Limewire pro 4.2.6

So I had a pretty bad surprise today :

I started Limewire as usually by clicking on its icon, but then it happened that it didn't start normally as allways, but it started like if I was instaling it for the first time. (I have absolutly no idea why, i just erased the LW installer(disc image), but didn't touch anything from the application folder) So the thing is that it restarted all from zero and with default settings, so with the downloads and incomplete files in HD>user>home. In fact I used to have them on the desktop, so I went in preferences to restaure this setting, I stopped and restarted Limewire. Then, on the contrary of "scottnsf", i didn't get any message, but in fact Limewire still does'nt recognize my incomplete files (they appear in library, but not in downloads) This is pretty annoying considering the fact that there were quite a few big & rare files that were loading for a while...

I tried searching manually for the same files, even found exactly the same ones (same name; size; id number), clicked load to see but even though it does'nt create an another file in the incomplete folder, it does start from 0% all over again...

I guess it has something to do with .dat files in the incomplete folder, but well, I'm a bit desesperate about it...
Any help would be great
thanks