I think this is because:
- the home directory is in some way encrypted with your password and when you 
log in, it gets decrypted
- when you change your password as root, the decryption-passphrase doesnt get 
changed to fit the new password because you do it as root
- your new password then doesnt work with the old passphrase

i do not know if it is a problem, when you change your password in the
"normal" way

greetz

-- 
encrypted home directory doesn't mount after password change
https://bugs.launchpad.net/bugs/579876
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