It is unlikely to be JRiver. Look into the software your universal remote uses.
I suspect what is happening is that your remote is set to toggle power on the PC, rather than turn it on. So what is happening is that the PC has woken up for some reason before you start trying to use JRiver, and when you press the button turn everything on, your remote software toggles the power off for the PC.
Many remotes just use the toggle power command rather than a specific "Turn on" and "Turn off" command. However, many also support the turn on/off commands. For example, my Harmony 880 supports both the toggle power and power on/power off commands. I have it set to always use power on and power off, so that if the PC is already awake, it just gets a power on command, which does nothing. When I finish with JRiver, the power off button on the remote always powers off (sleeps actually) the PC and turns off other components, so if it has gone to sleep while the TV and Receiver are still running, and I wish to turn those components off, pressing the same power off button on the remote just sends a power off command to the PC, which also does nothing.
I think you will find that is what happening to you. With the upgrade to Windows 10 your PC is probably coming out of sleep more often, checking for updates and so on, so the problem with using the power toggle command instead of the power on/off command will be more obvious.