Losing icons when duplicating a drive

I'm about to upgrade my Powerbook hard drive, so I've been duplicating (as distinct from backing up) the entire contents of my system drive to a Firewire drive, using Retrospect.
The drive replicates OK apart from some of the Spotlight database, which doesn't matter as it will rebuild anyway. I can then boot from the Firewire drive without any problems... except, all my system folder icons default to the standard blue folder. For example, /System loses the "X" on its folder icon, and /Applications loses the geometry set.
I've tried other applications apart from Retrospect to do the duplication, with the same results. Can anybody tell me how to restore these custom icons, or ensure they're duplicated properly in the first place, without going through and patching them all back manually?
By the way, I noticed the same thing happened when I used the same method to back up my hard drive under 10.3.
Thanks, David.

Hallo David. Welcome to the Discussions.
This happens when the links between files, folders and applications are broken. I suspect that if you click on one of these icons, you will be asked to choose the application.
This happened to me recently. All was restored to normal when I clicked on a blank icon and, when promped to choose an application, all the documents with that suffix appeared with the correct icon. It did not happen immediately; but when I logged out and back in, all was as it should be.
There are other issues that might be relevant. You might find this thread helpful in exploring them.
I can't understand why this might have happened in your setup. I use Retrospect all the time, also to a Firewire drive. But I have never tried to duplicate, as distinct from backup using Retrospect. I know that some users have found Retrospect troublesome in relation to Tiger; and one does have to have the most recent version, for 6.0 did not work with Tiger.
Hope that helps somewhat.
Yours,
Martin
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Powerbook 15-inch G4 1GHz Mac OS X (10.4.8) Several veterans that go on and on. 40gig, 3rd generation iPod

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I verified the HD (while booted from it) and it didn't tell me to do anything, I think it was fine [sorry to sound so dumb, I should have written the results down] it said it was okay so I assumed any errors had been corrected without me having to address them. Then I verified permissions, again this seemed to go okay, response was alright and didn't tell me to do anything.
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I had tried this twice before over the weekend and received the same 5 Execution Errors both times.
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+ Executing Immediate Duplicate at 18/8/2009 00:54
- 18/8/2009 00:54:19: Copying Macintosh HD…
18/8/2009 02:48:37: Comparing Portable_HD…
File “com.apple.LaunchServices-0140.csstore”: different creation date/time (src: 18/8/2009 02:18:36, dest: 18/8/2009 01:08:16), path: “Macintosh HD/Library/Caches/com.apple.LaunchServices-0140.csstore”.
File “com.apple.LaunchServices-014501.csstore”: different creation date/time (src: 18/8/2009 02:52:16, dest: 18/8/2009 01:28:34), path: “Macintosh HD/Library/Caches/com.apple.LaunchServices-014501.csstore”.
File “local.nidump”: different modification date/time (src: 18/8/2009 03:15:10, dest: 17/8/2009 04:27:43), path: “Macintosh HD/private/var/backups/local.nidump”.
File “asl.log”: different data size (src: 95,312, dest: 99,307), path: “Macintosh HD/private/var/log/asl.log”.
File “daily.out”: different data size (src: 852,248, dest: 850,530), path: “Macintosh HD/private/var/log/daily.out”.
File “mail.log”: different data size (src: 1110, dest: 987), path: “Macintosh HD/private/var/log/mail.log”.
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File “system.log.0.gz”: different data size (src: 4258, dest: 4178), path: “Macintosh HD/private/var/log/system.log.0.gz”.
File “system.log.1.gz”: different data size (src: 4178, dest: 1557), path: “Macintosh HD/private/var/log/system.log.1.gz”.
File “system.log.2.gz”: different data size (src: 1557, dest: 1013), path: “Macintosh HD/private/var/log/system.log.2.gz”.
File “system.log.3.gz”: different data size (src: 1013, dest: 5346), path: “Macintosh HD/private/var/log/system.log.3.gz”.
File “system.log.4.gz”: different data size (src: 5346, dest: 1690), path: “Macintosh HD/private/var/log/system.log.4.gz”.
File “system.log.5.gz”: different data size (src: 1690, dest: 4010), path: “Macintosh HD/private/var/log/system.log.5.gz”.
File “system.log.6.gz”: different data size (src: 4010, dest: 1187), path: “Macintosh HD/private/var/log/system.log.6.gz”.
File “system.log.7.gz”: different data size (src: 1187, dest: 1029), path: “Macintosh HD/private/var/log/system.log.7.gz”.
File “ntp.drift”: different creation date/time (src: 18/8/2009 03:40:28, dest: 18/8/2009 01:40:28), path: “Macintosh HD/private/var/run/ntp.drift”.
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Completed: 441743 files, 77.6 GB
Performance: 634.7 MB/minute (694.7 copy, 584.2 compare)
Duration: 04:10:09 (00:00:03 idle/loading/preparing)

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