why my Stratix board can't run unless nios

You need to reserve un-used I/O "as tri-state" in your quartus project settings.

To make this assignment in Quartus:

Go to the Assignments menu --> Device --> Device & Pin Options -->

Unused Pins tab, and select the option to reserve all unused pins "As

inputs, tri-stated".

Some background: The Nios dev boards have a feature for implementing

and demonstrating remote reconfiguration of the Stratix/Cyclone

device. This is implemented by a single IO which is connected to the

board's MAX7128 configuration controller - if the FPGA asserts this

IO, the MAX device will follow the power-on configuration sequence in

an attempt to boot the FPGA with (presumably) a new FPGA configuration

stored in flash. However, if this pin is not used in your design, and

is not reserved as tri-stated, the pin could (and does) float to tell

the MAX device to perform re-configuration.