I'm using a little App Store app called Backup Buddy which does a great job at keeping incremental backups. However, folders with custom icons show up without their custom icon, and a blank file named "Icon" next to it, like on this screenshot:

Now the lack of custom icons doesn't bother me on a backup, but it shows that something is not identical to the disk I'm backing up. So if this isn't identical, what else isn't?
I assume OS X uses the Icon file to store the custom icon, but doesn't display this file and instead displays the custom icon on the folder itself. Why isn't it doing just this on my backup? When Time Machine makes backups, everything is identical down to the last icon.
I'm also using Time Machine to back up other stuff, and since it can only do a single backup task, I have to use another app to backup other stuff, hence Backup Buddy.

Now the lack of custom icons doesn't bother me on a backup, but it shows that something is not identical to the disk I'm backing up. So if this isn't identical, what else isn't?
I assume OS X uses the Icon file to store the custom icon, but doesn't display this file and instead displays the custom icon on the folder itself. Why isn't it doing just this on my backup? When Time Machine makes backups, everything is identical down to the last icon.
I'm also using Time Machine to back up other stuff, and since it can only do a single backup task, I have to use another app to backup other stuff, hence Backup Buddy.