This is most likely due to the account not being fully configured.
Check to see if the status of the account is "Unknown" or otherwise not in a "Healthy" state. This means the account requires additional configuration and we cannot collect assets via our collection API since we do not have the appropriate permissions. When this is the case, we will derive the EC2 instance from your billing file. When an instance is derived from the DBR we will only show the tags that are present in the billing . file if the option within AWS to include all tags in the billing file is enabled. The best way to ensure all appropriate tags are included, configure the account within CloudHealth.
For information regarding how to configure an AWS account, see: Enable AWS Accounts in CloudHealth