Sadly, I don't have a Splunk AWS environment to compare with anymore which make this a little harder, but here's a few questions:
I assume you have the relevant saved searches enabled to generate the topology data? See https://docs.splunk.com/Documentation/AWS/latest/Installation/Savedsearches
If you believe the issue is from the Splunk AWS application or add-on, you can and should open a ticket with Splunk (it doesn't sound like you believe so, however)
Alternatively, if the issue appears to come from the AWS Config service (or account) configuration, you can hopefully open a ticket with AWS
That being said, if you can provide data about your issue from both your environments (one works the other doesn't if I understand correctly), that would help us help you.
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