I've had the same problem since win10 1809.
When I have multiple windows open it will pull up the last viewed window, losing MC focus.
I do not need to navigate away during the MC operation, just to move around with MC & other windows running.
e.g. I use the browser then switch to MC, run an op, wait for MC to complete it's task & then browser will pop-up.
BUT If I navigate up/out from the source dir whilst op is running I do not lose focus
I am suspicious of the VGA driver involvement in this as it appears more frequent on some AMD driver versions than on NVDA. I do not have enough different hardware to test this suspicion fully tho