Do the downloads to resume appear in your downloads-panel after you started LimeWire?

If that's the case a possible explanation could be, that you downloaded a grouped search result and LimeWire now resumes a similar file with a slightly different filename. If that's the case, the download will start from 0% again and it will create a new temporary file. This is a defect, indeed, and the LimeWire-team is trying to solve it by implementing another addition Gnutella protocol, the HUGE proposal, which will allow to identify similar files with different file names securely.

So far, I don't think it's an MacOS-specific bug, since the methods used to write and read the file are working with JRE 1.1.8.