This has got something to do with the 'Device Manager->Ports->USB Serial Port->Properties->Port Settings->Advanced...->Selective Suspend Idle Timeout(secs)' settings. At the default value of 5 seconds I cannot get the Atari to work with the emulated disks even after booting from one. Set at the maximum 3600 seconds it works properly. I would guess what is happening is the port is being sent to sleep after 5 seconds of no data throughput. Perhaps RespeQT needs to send some kind of keep alive signal to the port every second or so to stop 'Selective Suspend' kicking in. I guess if I leave the machines connected, switched on but idle for 3600 seconds it will again go to sleep and stop receiving commands from the A8.
Sadly I need to have 'Selective Suspend' enabled in these settings and the 'Power management' control panel applet in order to prevent the weird, maybe related, maybe not disconnection failure I described here some months ago.
For the record. I am using a home-made SIO2PC based on the Sparkfun FT232RL breakout board which otherwise works properly, even at POKEY divisor 0. I have installed (and removed and reinstalled many times over!) the newest official FTDI drivers.
I also cannot get Montezuma's fork with PCLink built in to work, despite the PCLink driver under SDX properly recognizing that a PCLink server is available. But that is another story for another thread!