I checked with another engineer that was experiencing the same issue. What we found was that the SoS index did contain data - but the default panel searches were not querying for the correct hostname. I.e. the events were being entered into the database under a different hostname than the one found in settings.
So for anybody else who has this problem, run the following search as hexx suggested:
index="sos" sourcetype="ps"
If events are showing up then SoS is working and changing the hostname in Settings -> System Settings -> General Settings may fix the problem.
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