Are you only running Kibana and ES on the VM? What does the CPU/Memory utilization look like on the VM, and are you actively indexing a lot of documents in ES with trying to run the report?
That timeout that you're hitting is currently hard-coded, and it's possible that if the VM is under a significant amount of load which is causing an atypically long amount of time for reporting to generate the PDF which is hitting the timeout. Recently, we had an internal user running ES/Kibana/Metricbeat/Filebeat all on a single VM which was indexing a large number of documents, which was causing that timeout to be hit.