Can you explain a bit more your observation in regard to the other serial ports on the card? In my case it does not matter if I'm using serial communication in the sketch or not. The simple LED blink sketch will not upload again after the first inital successful load. I have to completely exit the IDE, restart it and the sketch and imeadiately click upload to get one more sucessful upload. I saw a few post replys from Nick on another thread regarding the driver in Device Manager and mine are all normal and as expected. I also tried severl USB cables just in case since I'm familiar with signal integrity issues as that is my job.
Can you get a verbose display of the results in the lower status area of the IDE during a failed upload since I have not had time to get mine yet? Also, can you get successful uploads on the first launch of the IDE and imeadiate upload click like I can?