I've been working with Max and Arduino on and off for years and I've always had this problem but just lived with it.
So yes if I am sending data to the Arduino through the Serial object but decide I want to edit my Arduino sketch I send a close message to the Serial object and then upload the new sketch.
Sometimes this works fine but other times, Arduino gives me a 'Serial Port in use message until I quit Max'. So i have to save my Max stuff, quit Max, update my sketch, Open Max, load my patcher. Annoying!
I'm using 10.7.5 but pretty sure its been like this for ages.
It might not be a Max problem but then the fact that quitting Max sorts it out points towards the fact it is.