What cause this problem?

Okay, you just freaked me out. You've modified the Nios II CPU so that a call instruction to a special address causes data transfers between main memory and onchip memory?

Here's the way I would recommend doing this. Create a custom instruction that has an Avalon master interface. When you execute the custom instruction, have it perform the equivalent of a DMA operation and do the memory transfer. If you Nios II has a data cache and this data could have been in that cache, it needs to be flushed.