irkgreen,
I guess I was a little confused as to what exactly you had hooked up. The true/inverted setting is actually sent to the serial smart board itself. So it needs to be connected to the IO-204 to change that.
If all you need is serial output, have you considered using the "serial output over digital output pin" option? It gets over looked often since the serial board provides the same function and it was released first.
You may be wondering why a "serial smart board" even exists. It's necessary when serial input is involved. The IO-204 is doing a lot of things all at the same time. Listening for data on a serial port would require all of the processor's attention and keep it from managing the Ethernet stuff. The serial board basically acts as buffer for serial data. When the serial board receives data, it holds it in an internal buffer. The IO-204 checks with the serial board periodically to see if there is any data in the buffer to be passed on to the server.
We don't publish the specs on the "smart channel" protocol because it's not very useful by itself. Every "smart" device requires heaps of back-end code on our server to be configured and run properly. When you set a I/O channel for a servo board, for example, it lets our server know to load up all those libraries for your module and widgets.