So you have your hardware and software in the EPCS. You power up the board the hardware is sent to the FPGA, the Nios comes up and bootloader is run. The bootloader copies the program into the correct target memory. Then your application starts running but it can't access the EPCS (you are using the HAL to access it right?)
Here's a test:
-Program your hardware and the "memtest" software template into the EPCS
-Power cycle your board
-Connect to the JTAG UART without downloading software (in the Nios II SDK shell type "nios2-terminal" to do this)
-If the software actually booted you should have the menu from the application in front of you (data should be still buffered)
-Attempt a test of the EPCS device
Also can you give more specifics? Quartus version, Nios version, target board information, how are you trying to access the EPCS in software, etc....