Just to confirm, when you have DEBUG on for the agent, you see transactions listed for the messages, and the only difference is the timing when you have batching on and off?
If so, this is likely some kind of Spring concurrent execution handling we don't instrument. Are you able to look into this yourself, eg our current concurrency plugin has these apm-agent-java/apm-agent-plugins/apm-java-concurrent-plugin/src/main/java/co/elastic/apm/agent/concurrent at 2e40422635e573bf83da84c67a325d2bf629a91a · elastic/apm-agent-java · GitHub
Alternatively, would you be able to create a standalone example that shows the issue?