Have you tried run processors separately?
Have tied to System Library Properties in NIOS IDE (of your programs).
Check these parameters:
stdout:
stderr:
stdin:
there should be set to JTAG_UART or UART module.
Actually I do not recommend to use JTAG_UART component in multiprocessor mode. I got a lot of problem with it. Try to use UART.
Moreover in NIOS IDE environment meniu "Run" add run option that lets you run your application. Load JDI file. Next step "Target Connection" turn off NIOSII Terminal Communication device and use external UART terminal.
I am never succeeded connect NIOS IDE terminal to UART port of PC (strange).
After that try run your application for one processor... it should work.. if you did not made something incorrect in Quartus.