I suspect that the problem is your OS/Driver serial port is not allowing the DTR signal to be processed properly other then on it's initial opening. Failing to send the DTR auto-reset command to the board would give the error message you are seeing. I know that is not a solution but should allow you to focus on the most likely root cause of you symptom. You could prove this out by trying to use a manual reset switch at the proper timing when uploading and see if that works or not.
Lefty