I appreciate that this is an old thread but I've just come across it after having several months of this problem.
I'm using 1.8.10 on two PCs and both suffer from multiple instances of the same port appearing under Tools.
It makes Serial monitor and uploading impossible and the only way to get rid of it is to shut down all the sketches running on that IDE - affects all of them - and restart.
After plugging and unplugging the USB cable in several times, the number of COM ports with the same number start to increase under Tools. All are highlighted and all are ticked. Sometimes, up to 6 instances of the same port show.
I thought it was a board problem, but it's not. It affects all the boards I use, Uno, Leonado, Mega.
No other USB devices or applications have this problem.
I never saw the problem before in all the previous years going back to 2010.
I use powered hubs that have always worked well. Using COM ports directly off the motherboard makes no difference.
I've also noticed another problem which may or may not be related.
Plugging a USB cable into one board, causes another board to reset.
I've scoped the USB data lines and they are clean.
All that seems to stop it is to disable RESET, but that's a pain.
I can live with that one, but the multiple COM ports is seriously trying.
I wondered if there had been any progress on getting a fix.