The way to set the Communications Timeout for a particular printer in Simplify3D V5 is no longer where it was in V4. In V4, the input box sat at Tools ▸ Firmware Configuration ▸ Communication ▸ Configuration Timeout. That field appears to have been relocated, and the updated path or procedure for applying the timeout to any single printer is not yet evident. Correcting this is necessary because long diagonal extrusions still trigger the “Response Timeout” error.
Can you copy and paste the output from the Communication tab of the Machine Control Panel for when this message appears? It will help to see the commands around that point in time.