Closing the loop here: It looks like you need to create your KM Rewards account
before booking and taking the flights.
I received this email response:
Good morning XXXX,
Thank you for contacting KM Rewards and apologies for the late reply.
We wish to inform you that flights taken before the enrolment date are not eligible for Skybux accrual.
You enrolled as a KM Rewards member on 20 May, 2024 and your flights were before this date, therefore, regrettably, they cannot be credited to your account.
To ensure that your flights are automatically credited to your account, you must insert your loyalty number in your booking at booking stage or present it at the check-in counter at the airport. You may also enter your membership number during online check-in.
We wish to inform you that information regarding KM Rewards, how it works, and the terms & conditions should be made available on the KM Malta Airlines website soon.
We remain at your service should you require further assistance.
Regards,
XXXX