Could you share a stacktrace from the JVM agent to better understand what is happening during the communication? If possible, please share as well your apm-server.yml configuration file.
Also, if you suspect that the problem is related to certificate validation, you can temporarily disable this behavior by using the following property in the JVM agent:
-Delastic.apm.verify_server_cert=false
It might be helpful to isolate the issue and see if cert mgmt is indeed what is causing the problem.