I have a remote rsync with gpg encryption and can restore without problems on my thinkpad (FreeBSD) - but not on my MacOSX:

$ git annex whereis DSC_7615.JPG whereis DSC_7615.JPG (2 copies) 6855de17-c8fb-11e1-9948-f0def1c18073 -- thinkpad e388bcf6-c8fc-11e1-a96f-6ffcbceb4af4 -- backup (rsync xxxx) ok

$ git annex get --from backup DSC_7615.JPG fatal: Could not switch to '../../../.git/annex/objects/Pw/XP/SHA256-s1028494--SHA256': No such file or directory

git-annex: : hGetLine: end of file failed git-annex: get: 1 failed

$ git annex version git-annex version: 3.20120629 local repository version: 3