Very odd, but I've had a look into it and found the hidden chflag which hides files from the finder. It's used so that people don't see and interfere with files they're not ment to.
A quick fix (but which I don't like) is to make all hidden files viewable from Finder. To do this open terminal and type:
defaults write com.apple.finder AppleShowAllFiles TRUE
It's very ugly because all I want to do is see the downloads which are hidden, not every file. They're made invisible for a reason.
Looking more into it, it turns out that files can be flagged up as 'hidden'. This makes them invisible. So to make files hidden or not hidden in terminal you type:
chflags nohidden afilethatishiddenforexample.txt
or to make it hidden again:
chflags nohidden afilethatisnothiddenforexample.txt
Think I'll just have to log out and back in again to fix Google Chrome properly.