There is a special setting for the system console. The UART (either serial uart or jtag uart) that is selected as the system console is initialized at the beginning of the kernel init, and uses a special mode of the driver. Once a component has been opened that way, it can't be opened again through the /dev/ path and can only be used through the stdin/stdout descriptors.
I don't have an eCos installation right here, but if I remember correctly you can change the component used for the system console somewhere in the NiosII parameters in the eCos configuration.