Had a peculiar problem last week where the computer at home I use to pull backups from a remote VPS could not longer SSH into the remote system.
Permission denied (publickey).
rsync: connection unexpectedly closed (0 bytes received so far) [Receiver]
rsync error: unexplained error (code 255) at io.c(605) [Receiver=3.0.9]
After looking at directory permissions on both systems and user credentials as the possible source of the problem I came across this post where it recommends that permission for the private key file be set to 600.
chmod 600 ~/.ssh/id_rsa
The change in permission worked, perhaps the file had too high of a permission number which in not allowed. As to how this happen I have no idea, but I probably must have carelessly changed the permission at some point. This happen in a Debian Wheezy system.