In 6.1 where are the files actually stored that are to a Documents & Media folder? in 6.0 files were stored in the data directory in the liferay home directory.
This doesn't seem to be the case for 6.1. Is my assumption wrong about this?

These are managed by values in the portal.properties and portal-ext.properties. It's possible the default in portal.properties changed, but it's pretty easy to find out where they'd be now...

I figured out what the problem was and it was totally do to pilot error.

I had copied all the properties files from my dev setup including the new setup wizard properties file.

It sets the liferay home directory to what I had in dev, which is different from what I have for staging.

Liferay dutifully built the data folder in that directory and that's where I found my files. Duh!

Changing the liferay home in the properties file to what it should be for staging and moving the data folder to the same fixed my issue.