I think that's due to the bootloader of Leonardo.
When you first connect the board the first com port you see is the one used to upload the bootloader then thessecond one is the communication you get through the Serial command.
So if you have to upload a new sketch use com9 but if you have to communicate with the board use com10
Keep in mind to keep the serial monitor closed untill you see the com10 port, then choose the right port on the arduino ide and only after this open the serial monitor. If you keep the serial monitor open and a new com port is added I saw that the ide doesn't show the new port in the menu.
Of course when you have to upload a new sketch you must select the com9 port on the ide.
Anyway this is strange, try to delete and re-install the driver of the board. Do this while the board is unconnected