Using Scaler II with NIOS II

I assume that core comes with the Nios II macros you are using to access those registers. If so I would check to see if they have specific macros for each register, it makes things easier because you don't have to worry about register offsets because it's taken care of by the macro itself. Most (or all) of the embedded cores in Qsys have macros such as these. For example these are the macros used to read and write the IRQ mask of the PIO component:

# define IORD_ALTERA_AVALON_PIO_IRQ_MASK(base) IORD(base, 2) # define IOWR_ALTERA_AVALON_PIO_IRQ_MASK(base, data) IOWR(base, 2, data)

If the Scalar II core doesn't have such macros I would mention in your service request that they should probably be present.