Running the command
sudo rsync -a -e ssh /home/blah user@server:/home/blah
rsync seems to be renaming directories (not sure if it is renaming files). For example, "M.I.A." is being converted to "MPTBTC~C". This also happens when copying over samba.
The target file system is ext4.
Update: This appears to only happen with directories that end with a period. A google search indicates this should only be a problem under windows, but I am syncing from linux (ext3) -> linux (ext4).