TM Restore weirdness

I had to send my two-month-old iMac back because of screen problems. Before I did so, I backed it up to my Time Capsule via Time Machine, cloned the drive via CC to a FW drive, then Secure Erased the drive, changed the password, and returned the machine to its out-of-the-box state.
I received it back today. The first thing I did was to change the password back to my original one, and initialised the drive while booted from the install DVD. I then chose Restore From Backup. The Mac found the Time Capsule – but couldn't find the newly-initialised drive. After an hour of faffing around unsuccessfully, I had to connect the Firewire clone and reboot to it.
Then I started over – and the Restore From Backup app still couldn't find the iMac's drive. On a hunch, I powered down a Mac Pro that was ethernetted to the Time Capsule, then reversed through the screens until I got to the first installer screen. Finally, Restore was able to see the hard drive.
As far as I can tell, the Restore was largely successful except that I seem to have lost about 30-40 emails from my Inbox and I had to import the contents of all my existing mailboxes. I can live with that, although I'm pretty unhappy about losing mail.
The weirdest thing of all, though, is that now it has come time for my first post-Restore backup, Time Machine is backing up the entire drive. I made sure to rename the machine and the hard drive correctly so that this problem wouldn't arise.
Overall, I'm disappointed with Time Machine and Restore From Backup. What it's doing now is just a waste of time, energy, and my Time Capsule space. I wouldn't use it again for drive restoration, instead I'll revert to using CCC clones which have served me well in the past.
In fact, I may wipe the drive tomorrow and apply the clone I have, then trash the existing .sparsebundle on the TC and start all over again.
Not one of my better Apple experiences, I have to say.

Thanks for your response, Jeremy. From what you say, it seems that each time you do a System Restore through Time Machine, it will then create what is effectively a duplicate of the very backup you've just restored. IMO this is a waste of drive space, time, and energy.
Although I haven't had the time to try it yet, it seems, on the face of it, that every System Restore, no matter whether it's via Time Machine, Carbon Copy Cloner, SuperDuper, or Disk Utility, will trigger this duplication behaviour by Time Machine. Which is, of course, less than desirable.
Unless those invisible files which track file/directory changes for Time Machine are not themselves backed up by Time Machine – but are backed up in a clone. I'll have to test this...

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