analogWrite OR digitalWrite?

I've got a seeeduino mega and am trying to get it to talk to a Processing program running on my PC.
The problem I have is that depending on the firmata version I install on the board (standard, old standard, analog, digital, simple digital, simple analog or servo) I can either have analog outputs or digital outputs, but never both at once.
For example if I install standard firmata I can turn the LED on pin 13 on and off with digitalWrite and also control all the other digital pins, but I can't fade the LED on pin 13 with analogWrite.
If however I install install simple analog firmata I can fade the on-board LED on pin 13 using analogWrite, but I can't turn it on and off with digitalWrite. I also can't use digitalWrite to change the state of any of the digital-only pins.
Does anyone have any idea what the problem might be?

Does anyone have any idea what the problem might be?

Sure. Firmata is not yet supported on the Mega. Considering the fact that some Firmata sketches don't compile using 0021, I don't think the Arduino team really supports Firmata.

You can, of course, develop your own protocol, and learn something in the process.