Well, I know one failure mode that can cause that, it's rare but it's possible as it happened to me once.

See, if for some reason your device cannot mount /dev/mmcblk0p3 as /home on boot, then it will create a new /home for you off your /root partition. An indication to that is if the first boot after it happens takes somewhat longer as usual.

What's the problem with this: All the stuff that was on your /home is now not accessible, instead the device looks like "new", if you had any backgrounds set, or icons grouped into subfolders or anything, that is resetted to the way the device was in beginnig.

Your previous data is not lost, however. It's still on the partition that's just not mounted anywhere any longer

To see if that's the case, go to console and give command "mount | grep mmcblk0p3"

You should see something like this:

If you do not see the line above, then the problem is as I described.