Time machine missing files
Timeline
1. 11 days ago I buy a new 15" retina haswell macbook pro running mavericks, and a new 2TB time capsule.
2. Yesterday I returned the macbook pro because it was making creaking noises and had it replaced with a new one.
3. Now I try and restore my backup.
Story
I restored from my latest time machine backup by pressing CMD-R while booting and specifying to restore from the Time Capsule. It took a couple of hours over wifi and finally restored, when I came back to it, the machine had rebooted and I was at my normal login screen.
So I thought the restore had been successful at this point and I log in, however it asks me for my Apple ID login as if i've never entered it before (I have), and I have some new mavericks icons at the end of my dock that I had previously removed. I open up my terminal (i'm a web developer) and I notice its missing my custom prompt (oh-my-zsh) which I track down to the .zshrc file missing.
I check my databases and they are all corrupted. The MySQL error file is constantly spamming itself saying the data is corrupt and that it might be missing its binlogs. A number of my apps don't remember that they are licensed. The machine has forgotten most of my preferences such as tap to click, however it has remembered things like my desktop background and my safari preferences (they were not synced from icloud I made sure).
I dig into this a bit more by mounting the time capsule and having a look around in the terminal.
cd /Volumes/Time\ Machine\ Backups/Backups.backupdb
ls -lah 2013*/Macintosh\ HD/Users/jon
This prints out the contents of what the backup considers my home folder to be like at every backup (there were 23 backups stored over the 10 days). First backup being on the 2nd of November, most recent being on the 12th November.
I see that from the 7th my .zshrc went missing, it was not in any subsequent backups after that, so I tried restoring back to that date. After restoring my terminal preferences are back, but the databases are still corrupt and I notice other things missing instead.
I dig into it a bit more and list the files again.
Then I notice just how bad it is.
On certain backups it has missed massive numbers of files, including directories such as Downloads Library Desktop etc. Then they come back in the next backup, or go missing forever. I know time machine doesn't backup the entire computer each time, but I know that it should be creating HARD links in the filesystem, so that EVERY backup appears to be a complete system backup. This is not the case.
I can rebuild this new macbook pro to have everything I need on it again, but I CANNOT trust my £250 Time Capsule to take backups, in which case it becomes an extremely expensive router + hard drive.
I think this might be a bug in Mavericks, 10 days is not very long for backups to start going astray!
Is there any way I can repair this somehow? Has anyone else had this kind of problem? I phoned apple support and they just tried to guide me through doing a re-install, when I explained that the backups themselves seemed to be missing files the support agent just didn't seem to understand, not very helpful at all. As a fellow engineer I would prefer to speak to another engineer and I could provide all the diagnostics they could want, short of giving them ssh access.
MacBook Pro with Retina display, OS X Mavericks (10.9), Backing up to a Time Capsule