This is expected behavior with the Leonardo. I am surprised you did not see this behavior with your previous OS.
The Leonardo shows up as two different CDC devices. When the bootloader is running it shows up as a CDC device with a unique device ID and then during normal operation, it shows up as another CDC device with a different device ID.
Windows will see these as two different serial devices and assign a different comm port number to each one.
When uploading to the Leonardo, the IDE will reset the device to initiate the bootloader. That is when you see one of the ports disappear and the other port appear. Once the upload is complete, the sketch will run and switch to the previous port.
It's possible that on your previous systems, you had the same com port number assigned to each CDC device, so that it looked like the same port. However, you still should have seen it briefly disappear and then reappear during the upload.