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Without seeing and testing your code (which even the GitHub issue doesn't have) it's hard to make a judgement on what the actual cause is, but I can give some pointers.

ROS wraps DDS and in doing so it uses things like mangling rules to represent namespaces, topic naming patterns to help separate ROS topics and raw DDS topics, etc. It also uses a domain that may be different from the default domain of FastRTPS. Here are a few things you can check to get you started.

• Make sure that the ROS_DOMAIN_ID environment parameter is set so that ROS uses the same domain ID as your plain FastRTPS application is using, or set the domain ID used by the FastRTPS application to match the ROS one.
• Make sure that your plain FastRTPS application is using a topic name that the ROS application can see and understand. There is a design article about how ROS topic names map to DDS names. You can also find sporadic discussions about this via this issue search. If you are unsure of what topic names the ROS side is using, you could try listing all found topics from the FastRTPS side.