I'm not sure how, but I seem to have lost all my downloads in progress. I've found them in my library (incompleted), but when I click 'Resume', they reappear in the download box of the Search tab, but start downloading from 0% again, rather than their actual level. Some of the downloads were near complete, in one instance 94%, so it is a shame if I have to start from the beginning again. Is this normal, or can I somehow resume the downloads from where they left off.

Make sure that "# of days to save incomplete files" is set to something above 0. This can be found on OSX from Preferences -> Saving, and on Windows/Mac Classic from Tools -> Options -> Saving.

Alas, this is not the problem. I had already checked preferences, and I have it set for 7 days. I'm more concerned with not being able to resume from the current state of download, than them curiously disappearing into the library file, but thanks anyway.