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Box.com is still not working properly in version 5.20140227 (I'm using it in Debian testing and sid).
I created a new clean repository and configured Box.com (everything from the webapp). At first it seamed to work, files where being uploaded and the logs where fine. Then I created another clean repository in another computer and started syncing. Downloading files worked properly, but when trying to upload a file from the second computer I got this:
copy my_file (gpg) (checking box.com...) (to box.com...)
100% 0.0 B/s 0sResponseTimeout
failed
git-annex: copy: 1 failed
When I got back to the first computer I saw the same behavior, uploading files wasn't working any more.