Hi Nir,
it looks like there is a problem with generating this script in the case of EPCS devices. To work around this, you can extract the correct command to use from the Nios II IDE using the method I described in my previous post. You can then run that command directly from an SDK shell (or create your own script).
As you said earlier, there is currently no driver for the EPCS device in eCos. This means that you will not have read/write access to it from your application. However a driver of this kind is not required for you to use the EPCS as a boot device.