One possibility is that you’re working for a research agent rather than a security/distribution/mining agent. They give RP instead of LP. You can check your Journal to see if you have any research points - they haven’t been moved to the new wallet.
Edit: another possibility is that the Core agent is a storyline agent. Storyline missions do not award loyalty points.
No research points shown in Journal but just started the Sisters of Eve arc and not getting LP’s for these missions either. After your suggestion I tried a vanilla mission from another SoE agent and got LP’s this time - so you’re right, seems to be the mission type that affects this. Thankyou