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DE0-Nano-SoC peripherals not updating values when running

I am programming a DE0-Nano-SoC by building a Nios II system in Qsys and programming the system in C in Eclipse. I have been running into a problem where my GPIO pins, switches, and any other peripherals are able to input or output the correct values at the start of me running my code in Eclipse, but as the code continues to run, the values do not update, or they update after a few minutes. For example, a clock that I am outputting from a GPIO pin with C code does not switch between 1 and 0, it just stays at the first value the code set it to. When I use my C code on an example University Program system in Altera Monitor Program, the output is a correct clock, so I know it is not my code. This is my Qsys system:


Here is the most recent test code I did with this, I was running code that is supposed to print the values on the switches. I was flipping the switches as the code was running, and the value initially on the switches was still being printed even as I was changing the values on the switches.

aaa.PNGAny ideas on what could be going wrong?

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