Yosemite install has messed up my home folder after fixing user short name.

I just installed Yosemite 10.10.2 onto a new Mac Pro, replacing 10.9.5. After the installation completed, I allow my iCloud settings the set things up for Mail and my other general account settings. The only issue is that when I changed my short name from timjones to tjones, auto correct changed it to tones (as it has done in this post 2 times). Once I recognized this, I used the normal method for modifying a user account by logging in under another admin account, using ditto to copy the '/Users/tones' folder to '/Users/tjones', selecting the Tim Jones account in Users and Groups and using the Advanced Options to reset the short name to tjones. I then reassigned the home folder to /Users/tjones.
All seemed to go well and when I logged back in as tjones. However, I could no longer set up my preferences for apps nor could I access my mail. I then clicked on the 'tjones' home folder in Finder and was greeted with a dialog that said 'Preparing to duplicate items to "Users"'. It then spun for around 2 minutes and prompted me for my password. I entered it and the dialog changed to 'Duplicating 0 items to "Users"' and it's now been spinning for around 15 minutes.
What is this and am I back at square one and reinstalling (I have good backups...)?

The "Duplication" finished finally and my home folder has now disappeared from the /Users folder in Finder. If I check in a Terminal, there are now 2 folders - 'tjones' which is set to tjones:wheel and 'tjones copy' which is set to tjones:admin. As mentioned, neither is visible in Finder.

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Yosemite install has messed up my home folder after fixing user short name.

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