Seems to be the old replies were delivered after the timeout. Actually this indicates there is a problem at the client. Usually this is caused if the client side session thread pool is out of threads because e.g. all threads stuck in onMessage delivery. If now a request times out and the replies were already in the session pool's input queue but can't be delivered due to waiting for onMessage completion, they will be delivered when the next request is sent.
Increasing the max threads of the session pool should help. Look
here. In a recent release we have increased the max threads to 50.