I am running DNN version 3.1.1.  I have uploaded files into the Documents module, and then downloaded them and the behavior is completely different then when downloading from the Repository module.

I am noticing a similar behavior in the File Manager.  The file manager download window stops transferring, though the window stays open.  With the Repository the file stops transferring then the download window closes, acting as though it is done.  Is this some kind of download timeout or script timeout that maybe I need to update somewhere?

groggu, I did some more checking and there's a good chance my site may not be valid for pointing out the problem you're seeing. That site isn't running an up to date Repository (haven't had time to upgrade anything lately). I just did some tests on my development computer (which has 3.0.16 installed) and Firefox didn't blink at downloading .zips, pdfs, etc. I'm planning on upgrading my personal and hosted sites this week as soon as I can test upgrading them on my development computer.