Finally figured this out. The problem manifests with the combination of queue visibility timeout (2 mins) and the scheduledExecutor delay (5 mins).
Increasing the visibility timeout to 15 mins solved the problem.
My theory is -> The AmazonSQSBufferedAsyncClient retrieves message and keeps it in the buffer waiting for receiveMessage call. As the executor delay is 5 mins, the visibility of the message times out befor receiveMessage is called and the message is returned to the queue. It also looks like the message is picked from the queue almost immediately. And now for whatever reason a call to receiveMessage does not receive the message. Increasing the timeout which gave a chance for the receiveMessage call to happen before a timeout event, solved the problem, I guess.
Any other possible explanation?