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The symptoms you are describing aligns to the github issue. Are you able to workaround this issue by manually associating the same User referenced via CloudFormation User Profile with the Domain. Ignore the error you will see when doing this action, but internally it will call AssociateProfile API. Also, can you confirm whether you are using domainID in the CloudFormation template:
UserProfile:
Type: AWS::SageMaker::UserProfile
Properties:
DomainId: !GetAtt StudioDomain.DomainId
UserProfileName: !Ref UserProfileName
UserSettings:
ExecutionRole: !GetAtt SageMakerExecutionRole.Arn
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I did use the domainId in my clouformation, here is the code snippet, but I'll also tried the workaround to see if it works.