Configuration warnings with clean 0.3.2 -> 0.4 upgrade

To reproduce:

- start with clean Python install, no ``.astropy`` folder in home directory
- install astropy 0.3.2 with e.g. ``conda install astropy=0.3.2``
- install astropy 0.4 with e.g. ``conda install astropy=0.4``
- start up python, then ``from astropy.io import fits``, gives:

```
WARNING: ConfigurationChangedWarning: The configuration options in astropy 0.4 may have changed, your configuration file was not updated in order to preserve local changes.  A new configuration template has been saved to '/Users/tom/.astropy/config/astropy.0.4.cfg'. [astropy.config.configuration]
```

I've also seen the same error as this person is reporting:

http://stackoverflow.com/questions/24852262/astropy-deprecation-warning

with a slightly different upgrade path (can't remember exactly how!) on a machine on which I had not edited ``astropy.cfg``. To repeat their error:

```
WARNING: AstropyDeprecationWarning: Config parameter 'enabled_record_valued_keyword_cards' in section [io.fits] of the file 'C:\Users\nandhos.astropy\config\astropy.cfg' is deprecated. Use 'enable_record_valued_keyword_cards' in section [fits] instead. [astropy.config.configuration]
```

Might the two be related?

cc @mdboom