I think I know now, what your problem is, and it might not have been solved yet, indeed.

Ok, LimeWire groups files in the search results, even if they don't have the same name.

If you have a group of 10 differently named files in your search results and click "Download All", LimeWire, when it is restarted, will just resume one of those files. - If the file you downloaded previously had a different name, it won't be resumed, but a new temporary file will be created on your disk.

There is only one solution I can offer: If you have a group of search results in your search panel, do not download the whole group, but only one file. Since LimeWire will automatically requery the network, it will be downloaded even if the specific host you were trying to download from wasn't available. This should prevent LimeWire from creating multiple temporary files for one download.