Identical drives reporting different size/files

[macstatic]

If I have two identically sized external hard drives (though different brands/models), then copy the entire content of drive #1 over to drive #2, shouldn't everything be exactly the same?
I've used Chronosync to copy the entire drive, yet everything (except "Capacity") differs slightly. Chronosync was set to "Synchronize deletions"-"When deleting files: Delete immediately". I believe this should ensure identical copies (not creating an archive of differing files/folders).

Below is what Disk utility tells me about the two drives (I get more detailed information there than OSX's Finder "Get info"):

Drive #1:
Capacity: 2 TB (2 000 054 960 128 Bytes)
Available: 395,99 GB (395 986 948 096 Bytes)
Used: 1,6 TB (1 604 068 012 032 Bytes)
Number of files: 114 294
Number of folders: 2 810

Drive #2:
Capacity: 2 TB (2 000 054 960 128 Bytes)
Available: 395,91 GB (395 912 454 144 Bytes)
Used: 1,6 TB (1 604 142 505 984 Bytes)
Number of files: 114 415
Number of folders: 2 811

I've used the terminal to check the root of each drive's contents (ls -al") but they both report the same files/file sizes. I've also disabled Spotlight for both drives and emptied the trash. Both drives verify OK in Disk Utility.
I'm running OSX 10.6.8.

 

[dyt1983]

edit: To remove personally identifying information not relevant to the thread.

 

[macstatic]

Thanks for clearing that up, so I don't necessarily need to worry.

But the file/folder count is different so how to do I fix this problem?
Using Deltawalker (a file/folder comparison tool) I found some differing invisible files (a couple of ".download" or something similarly named (empty) folders within some of my normal folders which I deleted from the backup (they weren't present on the original drive).
Likewise I messed around with the Spotlight indexes, first using Spotless and messing around with its "Disable indexing", "Delete 10.6 index files" and "Delete entire index directory" features on the backup drive. Each time I had made some changes I started a new backup, hoping the source drive would make the backup drive the same, but without succeeding.
In the end I used the OSX Terminal to delete both the trash and Spotlight files. Also the Time Machine files, temporary items and Adobe Bridge sorting files on the backup drive as follows:

$ sudo rm -rf .Spotlight-V100/
$ sudo rm -rf .Trashes/
$ sudo rm -rf .fseventsd/
$ rm .com.apple.timemachine.donotpresent
$ rm .com.apple.timemachine.supported
$ sudo rm -rf .TemporaryItems/
$ rm .BridgeSort

Again, following this "cleanup" I performed yet another Chronosync backup (hoping the deleted files would be replaced with copies from the source drive and/or rewritten by OSX. So I checked with Disk utility but still have differing results:

Hard drive #1:
Number of files: 114 346
Number of folders: 2 808

Hard drive #2 (backup):
Number of files: 114 394
Number of folders: 2 811

Although the top level of your drives may match, the directory structures under these might contain numerous files that Chronosync isn't matching. I normally start with an image copy (made using dd) and then use the command line rsync program because it is mostly "Mac agnostic" and (mostly) doesn't know or care about those Mac-specific files, and just makes a complete backup.

What's "dd"?
Do you suggest I completely erase the backup drive (using Disk utility), then perform a new backup? It'll take ages to complete, but I'm more than willing to do this if it's necessary to ensure that I have a fully working backup.

 

[dyt1983]

edit: To remove personally identifying information not relevant to the thread.

 

[macstatic]

Looking good so far!
Thanks for the suggestions -I've followed them step by step and Chronosync has been backing up all night. It should be done in a few hours so we'll see then how the two drives compare this time around.

The (external) drives are both connected via Firewire 800 to a Mac Pro.

I noticed (using ls -laF in the OSX Terminal) that the source disk contains Desktop DB and Desktop DF. According to what I've read this dates back to the pre-OSX days where file-types were identified by resource forks. I have no idea why these files were created on the drive in the first place (on second though, it could be because I turned on some "MacOS 9 compatibility" feature back in the Rosetta days. I certainly don't need it now).
Can I safely delete these files from the source drive, or will that mess up something else? I removed them from the backup drive and it didn't seem to cause any problems....
On the backup drive these files are missing and don't seem to be recreated (so far).

 

[macstatic]

OK, the backup is done and here's what I got from Disk utility immediately after Chronosync was done:

Drive #1 (source):
Capacity: 2 TB (2 000 054 960 128 Bytes)
Available: 396,28 GB (396 275 724 288 Bytes
Used: 1,6 TB (1 603 779 235 840 Bytes)
Number of files: 114 084
Number of folders: 2 796

Drive #2 (backup):
Capacity: 2 TB (2 000 054 960 128 Bytes)
Available: 396,28 GB (396 275 724 288 Bytes)
Used: 1,6 TB (1 603 779 235 840 Bytes)
Number of files: 114 083
Number of folders: 2 798

The available and used space is exactly the same! But the file/folder count is very slightly different. I did a "Get info" of the main folders on the root of each drive and they matched exactly (both size and file counts) so this is a major improvement over before. But I'm curious as to why the two drives aren't 100% exactly the same as in theory it would make sense they'd be.