As it's a USB connection you should never cycle the SPROG power without also restarting JMRI. The timeouts indicate that is taking a while for JMRI to receive replies. I've only seen this on slower systems such as Raspberry Pis. I don't think they are the problem.
Can you control turnouts if you set the SPROG to programmer mode?
Are you using the correct system name for the turnouts?
Andrew
