Nios board would work with SignaltapII

hi:

The board i use is nios pro stratix 1s40,when i program my sof file down to the FPGA, it just ok.

but then i use signaltapII to debug my froject, the case is that it often reload the sof file from the flash device, as i have set the unused pins as input & tri-state, it just impossible .The more strange is that sometimes i change something , like the input clock or some signal, it just could work.

ask for help, thx!