IRQ not working

Quite possibly since, IIRQ, the interrupts to the nios itself are level sensitive.

I'd guess that you need to read the edge capture register to find which bits have changed, then write back the same value to clear the bits.

It might be easier to see how the hardware registers work if you use a program loop instead of the interrupt. A first cut would be to loop for about a second, read and print the registers, then repeat. Once that is working just look for changes. Then try using the isr.