After running yet another fresh install i got the first 8 entries mentioned in @christoph-farnleitner, but nothing more. Still couldn't get the site to load. As a last ditch effort, i copied the code over to a wamp server on the same machine and it fired up first time, so issue definitely seems to be server related. When i tried copying over the DB from wamp to vagrant, I ran into some mysql errors that weren't being logged/displayed on the installer. So after going round the houses several times, it appears that the issue was actually to do with the mysql conf settings.
I'm using mysql 5.7 which out of the box doesn't seem to like the default date values from the magento installer and it was these dates that were causing the data to be missed. It affected several tables, not just core_config_data, but that was the most obvious one.
Running the install from command line worked, so this told me that it was a server config issue.
After more digging around, it appears that strict mode on MYsql 5.7 doesn't like magento default dates, so the fix was to add: