Hi, I have similar problem too with Mega.
When I send data to arduino straight from IDE,where I told him to blink LED on pin 13 it si runnig correct, but , when I send data by help of as3 glue and flash, RX LED si blinking,but LED on 13 pin isnt. Also I tried to set EVERY pin to ouput and set them to HIGH and nothing happens. If someone could help, I will be happy ever after until death.thanx