rsync command line to optain a bootable snow leopard clone

Did you Bless the System Folder after the Clone?

sudo bless --folder "/Volumes/Clone of Macintosh HD/System/Library/CoreServices"

I use the following rsync options:

/usr/local/bin/rsync -aNHAXv --one-file-system --fileflags --force-change --delete 
--exclude='.Spotlight-V100' --exclude='/.fseventsd' --exclude='/Volumes/*' 
--exclude='/private/var/vm/*' --exclude='/private/tmp/*' 
--human-readable --stats --progress "$source" "$destination"

You may need to compile rsync 3.0.6 as follows (see: also http://discussions.apple.com/message.jspa?messageID=10383609#10383609 )

Follow these instructions in Terminal on both the client and server to 
download and compile rsync 3.0.?:
Download and unarchive rsync and its patches
 Move patches directory to rsync-3.0.?
 cd rsync-3.0.?
Apply patches relevant to preserving Mac OS X metadata
 patch -p1 <patches/fileflags.diff
 patch -p1 <patches/crtimes.diff
Configure, make, install
(note: creation times are not preserved in x64, so…)
 ./prepare-source
 CFLAGS=-m32 CPPFLAGS=-m32 CCASFLAGS=-m32 ./configure
 CFLAGS=-m32 CPPFLAGS=-m32 CCASFLAGS=-m32 make
 sudo make install
Verify your installation
 rsync --version
By default, rsync will be installed in /usr/local/bin. If that isn't 
in your path, you will need to call your new version of rsync by its 
absolute path (/usr/local/bin/rsync).

Also, be aware that rsync 3.0.6 does properly not handle the metadata for the new HFS+ filesystem compression.

Sub-test: creation time ... ok
Verifying: hfs-compression ...
Sub-test: decmpfs xattr ... not preserved
Sub-test: UF_COMPRESSED flag ... not set
Sub-test: file contents ... match
Sub-test: creation time ... ok
Sub-test: modification time ... ok
Sub-test: hard link inode ... ok
Sub-test: hard link decmpfs xattr ... not preserved
Sub-test: hard link UF_COMPRESSED flag ... not set
Sub-test: hard link modification time ... ok
ok
Verifying: hfs-compression_large ...
Sub-test: decmpfs xattr ... not preserved
Sub-test: UF_COMPRESSED flag ... not set
Sub-test: file contents ... match
Sub-test: creation time ... ok
Sub-test: modification time ... ok
Sub-test: hard link inode ... ok
Sub-test: hard link decmpfs xattr ... not preserved
Sub-test: hard link UF_COMPRESSED flag ... not set
Sub-test: hard link modification time ... ok

What are the exact implications of this ? Could this be the problem ?

It won't be the problem, but System Files and some App's will have incorrect MetaData. CCC says that it handles this correctly. (Hopefully rsync will be updated soon)

For a good explanation, see: http://arstechnica.com/apple/reviews/2009/08/mac-os-x-10-6.ars/3

One thought, if you ⌘I the clone, do you have "Ignore ownership on this volume" Unchecked?

Is there a command line to uncheck "ignore ownership on this volume" ?
Just to be sure that it is all the time the case (if I change external hard disk for instance).

vsdbutil -d /Volumes/Clone of Macintosh HD

however, please note that the vsdbutil command is deprecated.

Here's a script that will test it:

/usr/sbin/vsdbutil -c /Volumes/Clone of Macintosh HD | grep -sq "enabled"
 if [ $? -ne 0 ] ; then
 echo -e \aPermissions on /Volumes/Clone of Macintosh HD are disabled. 
 \nUncheck 'Ignore ownership on this volume' for /Volumes/Clone of Macintosh HD
 exit 1
 fi

And the Man Page:
VSDBUTIL(8) BSD System Manager's Manual VSDBUTIL(8)

NAME
vsdbutil -- manipulates the volume status DB.

SYNOPSIS
vsdbutil [-a -path]

vsdbutil [-c -path] [-d -path] [-i]

vsdbutil [-h]

DESCRIPTION
vsdbutil manipulates the volume status DB. The following options are
available:

-a adopts (activates) on-disk ownership on the specified path

-c checks the status of the ownership usage on the specified path

-d disowns (deactivates) the on-disk ownership on the specified
path

-i initializes the ownership database to include all mounted HFS+
volumes

-h prints out a simple help message

The vsdbutil command is deprecated.

FILES
/var/db/volinfo.database Database of volumes managed
via vsdbutil.

SEE ALSO
diskutil(8), mount(8)

Darwin December 19, 2001 Darwin