On dos you own the machine down to bare metal for better or worse, usually worse, but software only slows things down.
I suspect if you stuck a protocol analyzer on it you'll find one of three situations:
Someone did simplistic polling instead of a windowing protocol so increased latency makes the overall system unusably slow. 0.1 ms vs 10 ms per handshake is not noticeable to humans but if your scada sequentially polls 10000 parameters thats the difference between a poll taking 1 second or about two minutes...
The other scenario is keep alive signaling where the computer needs to assure the CNC machine that its still alive and sane every 10 ms or the controller initiates an emergency shutdown. Can't have a giant lathe or printing press running off wild not under active computer control. So windows wants to multitask and do who knows what for 50 ms, and the scada shuts down.
The final situation is they're doing something "weird" at the hardware level like signaling over the control pins instead of over the serial ports. Like toggling the RS-232 DSR pin turns on the milling machine motor for 10 ms instead of sending a serial RX/TX power command every 10 ms. Windows opinion of DSR, IIRC, is DSR means the serial port driver registered in windows and is not available to end users. Been a long time since I've had to deal with that so I might misremember.