Turns out Sphinx will not read modifications to config files for a realtime index after it's been created: see here for info.
The way around this is to:
sudo service sphinxsearch stop
Then delete all index files (for me held in /var/lib/sphinxsearch/data/
):
sudo rm main_sphinxalert.*
Then restart service:
sudo service sphinxsearch start
This means you lose your existing index, which will then have to be manually rebuilt from your database.