Strange effect with Stratix FPGA

Why don' t You import the Pin Assigment from a sample design for the development board You are using and modify only the Pin assignments specific to Your design. I have been working with a CYCLONE Development Board sample designs which also shows how to place the LAN Controller in a quiescent state.

When using development board to host my custom design, I found always usesful to open an existing sample design delete their logic and implement my logic; this clears all the board interfacing issues (inlcuding FPGA configuration issues) and allows me to focus on the actual design that I am trying to prototype.