Deleting the ne_ruins.zip in the download folder does not work? Worked for me every time so far when I got that error.
Guys, it helps neither you nor me if you just report that “some zip file” did not work. We need more details. ISPs, regions, Java versions, etc etc 
Hi. I’ve had the same issue with some larger files (Nehahra, Quoth, Warspasm) over the past week or so.
I’m using Windows 7 Pro (64 bit) with the latest Java installed (updated last week). I’m with Virgin Media and have a 50Mb connection. It’s a fast and robust connection for everything else I download. Also, I’m based in the UK. 
Hope that helps. Between Simple Quake Launcher and Quake Injector Quake has never been easier to play and I really want them to continue!
Good luck.
Addendum:
I’ve downloaded a couple of the soundtracks from this link:
https://www.quaddicted.com/files/music/
I’ve had the same issue (broken files) and have had to download a few times before getting a full zip. Looks like it’s not necessarily a Quake Injector issue.
PS: Created a second post just in case you’d already read the above post and wouldn’t see an edit.
This should hopefully be fixed now, I switched from lighttpd to nginx as reverse proxy. Please tell me if there are any issues.
It’s working again!
Whatever you did, it definitely fixed the issue. Downloaded 20 files successfully in a row, 10 big and 10 small ones, from 1996 to 2015, using both Injectors, from 2 separate windows setups (via wi-fi and ethernet). Here’s the list:
arcdemo.zip
arcextra.zip
czg02.zip
digs03.zip
dxm2.zip
egany.zip
elektra.zip
fmb_bdg2.zip
func_mapjam2.zip
func_mapjam3.zip
honey.zip
jailbrk.zip
kaahoo1a.zip
mexx7.zip
pyramid.zip
retrojam2.zip
retrojam3dlc.zip
rrp.zip
something_wicked.zip
trincasp1.zip
No problem whatsoever. Smooth downloads and installation, as it used to be. Order in the Universe has been restored.
F U lighttpd! (whatever that is)
Thanks so much, Spirit. Thanks for taking care of your fellow quake marines. The 20th anniversary is coming, we should be replaying the best modern creations and the classic ones in preparation for that lovely event.
What a great gift for the holidays. Chthon is pleased with your offering.
Excellent! Thanks for reporting in.