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This is normal. The confusion is over the way that the "user files" option works.
It looks at the source volume, and only 'selects' files from /Users. This selection mechanism is controlled by the backup script: "all files" vs. "user files" vs. "sandbox", etc.. When writing files to the destination volume, if a file is on the destination but has not been selected from the source volume, it will be deleted from the destination. So, even if the file exists on the source volume, if it is not selected for copying, it will be deleted from the target volume (if it exists there).
What this means is that when you run a "user files" backup to a volume that previously contained an "all files" backup, all the files except for your user files are deleted (important stuff like the OS!).
The "make it bootable" step at the end is a technical detail involving the bless command. It is there because if you just make a plain file-by-file copy of a bootable volume to another volume, that new volume will not be bootable until it is blessed as bootable. This involves putting some data in a special place on the disk (somewhere outside the normal filesystem) where the machine's boot firmware (OpenFirmware or EFI, like the BIOS on old(?) DOS/Windows machines) can find it. If you used DOS, bless is analogous to the SYS DOS command.
If you want a backup to be actually bootable, you always need to use "all files".
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