I have the same issue, you can partially download a file and then exit Limewire and when you turn it back on, it will never resume from the last byte downloaded but instead it will download from the beginning. The incomplete parts exist in the incomplete directory.

This is the registered Limewire Pro by the way. I was expecting that technical support should be directly via email to Limewire staff, but instead it looks like it's via this forum. What gives?