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You do not use it, fine. I am quite sure that with the altmemphy based DDR2 controller, a reset_n signal appears in the SOPC Builder. It may appear even with the uniphy based controller (never used it). Are you sure this reset is correctly connected? If left floating or grounded it may give a reset to the controller, I am not sure that the controller while in reset do not asks for a system reset.
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Does the reset_n signal you said affect downloading the program?
I know it affect simulation