Ive tried the RTS method. It takes quite a while to turn on using software. Im only talking a few ms but its still enough to cause problems.

I think a circuit based on that scematic would be best. I dont have any logic gates that i can make a NOT gate out of so i cant test it yet.

I will have a go at the control characters method. That one seems like it should definately work aslong as i can program it properly. At the moment it relies on counting the bytes that arrive. With the control characters 1 or more will be missing.