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: <file descriptor: 6>: hGetLine: end of file
failed
git-annex: get: 1 failed

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