При DEST -- локальная машина, не работает ключ --compare-dest (и, подозреваю, 
что и --link-dest). Эффект повторяется при SRC в любом виде (SRC, [USER@]
HOST::SRC и rsync://[USER@]HOST[:PORT]/SRC )

Steps to Reproduce:
[wise@ipsec ~/tmp/test/1first]$ rsync -a --stats rsync://localhost/backup .

Number of files: 2
Number of files transferred: 1
Total file size: 31 bytes
Total transferred file size: 31 bytes
Literal data: 31 bytes
Matched data: 0 bytes
File list size: 56
Total bytes written: 88
Total bytes read: 167

wrote 88 bytes  read 167 bytes  510.00 bytes/sec
total size is 31  speedup is 0.12
[wise@ipsec ~/tmp/test/1first]$ cd ../2second/
[wise@ipsec ~/tmp/test/2second]$ rsync -a --stats rsync://localhost/backup . --
compare-dest=~/tmp/test/1first/

Number of files: 2
Number of files transferred: 1
Total file size: 31 bytes
Total transferred file size: 31 bytes
Literal data: 31 bytes
Matched data: 0 bytes
File list size: 56
Total bytes written: 88
Total bytes read: 167

wrote 88 bytes  read 167 bytes  510.00 bytes/sec
total size is 31  speedup is 0.12
[wise@ipsec ~/tmp/test/2second]$ rsync -a --stats rsync://localhost/backup . --
compare-dest=~/tmp/test/1first/

Number of files: 2
Number of files transferred: 0
Total file size: 31 bytes
Total transferred file size: 0 bytes
Literal data: 0 bytes
Matched data: 0 bytes
File list size: 56
Total bytes written: 68
Total bytes read: 92

wrote 68 bytes  read 92 bytes  320.00 bytes/sec
total size is 31  speedup is 0.19
[wise@ipsec ~/tmp/test/2second]$ rpm -q rsync
rsync-2.6.0-alt1