Sorry does this mean that bitcoin-qt 0.9.0 doesn't automatically access the .bitcoin/bitcoin.conf file from the users home folder like 0.8.6 does?
It does, but it doesn't parse -datadir specified in the configuration file currently (see issue
https://github.com/bitcoin/bitcoin/issues/3905).
The recommended way to use another data directory is to use -choosedatadir, which will store the data directory in the registry.