TD :
I know we touched on this briefly in chat, but if it works the same as IE, there may be something worth looking at.
When you download in IE, it puts the file in a temporary folder, defined in the registry - note this is NOT the same place as the file ends up.
So, Bloggs does his homework, says "This 10Mb file won't fit on C: as there's only 2Mb left, so I'll stick it on D: where there's loads".
What happens - IE downloads to a temp folder on C:, stuffs up, and unless you dig a bit you've no idea it's doing it.
Worth checking, and if it's not that, don't know.