I have also had the situation where MissionPlanner did not pop up the “Unplug … ok” dialog but when I noticed it was searching, I unplugged anyway to put Pixhawk in bootloader mode and it worked, of course.
That has happened to me more than once but I can’t say what particular circumstance.
Yep I am new to this game and wanted to put the Rover firmware on my Pixhawk about 2-3 weeks ago. Nearly pulled my hair out as it wouldn’t work on any PC in the house (all Windows 10 machines), so I went into the shop and tried it on an older Windows 7 machine and it updated no problem. All future updates will be done on this Windows 7 machine in the shop now, am I ever glad I didn’t update all my machines to Windows 10!