Nios II: The system console model is invalid.

I often observed this behaviour in two situations:

The first one happens when I first load a design, then I load a different one without closing the previous Nios console window. Although this seems not to be your case, all I need to do here is closing the old window.

The second one is more subtle: it happens when I saved the previous design in a NV memory (epcs or whatever) for automatic boot upon power up. If you then load with jtag a newer design having the same base epcs address, the OLD Nios firmware would indeed boot from epcs and this could lead to the inconsistency error. The solution is making sure epcs is blank when you switch to a new design.