It is very interesting. I need more information on this.
I've used this board on a number of different machines but never has it showed up as two different ports.
I used a USB hub to add extra physical USB ports as the board had been plugged in each one (just in case) and when I pugged it in I got a windows notification in the lower left corner of the screen saying it was configuring arduino yun. (good sign?) then is said it was ready, so I sent an upload and the same exact thing happened.
So I tried in on an other port of the hub and again it said configuring. I clicked on it, took me to win10 settings app. It seems to recognize the yun as a keyboard judging by the icon next to it.
If it's a problem with the bootloader, would "burn bootloader" help? I have no idea what it really does and I don't own the board, it's my school's.
I have managed to upload from this computer and very probably to this very card
If by the same thing, you mean you heard the disconnected sound, then that means the "normal" port is being closed.
What sketch is currently loaded on the Yun?
Perhaps loading a standard sketch (Blink?) will make it work properly? Oh, wait, you're having trouble loading a sketch... (more on that idea in a moment.)
try loading a sketch over the network (wireless WiFi or wired Ethernet, it makes no difference.)
I have noticed a SD card slot underneath the yun. is that a way to upload code? export compiled to the card then put it in.
I have tried plugging it into my computer's ethernet port with both a direct cable and a cross-over as well as onto my internet box (with both also) and I didn't detect it. do you need to set up something for it to work? am I missing something?