NIOS II processor Not responding

I would agree w/ Frank's suggestion. Whether it's Nios, DSP Builder, or any other piece of MegaWizard IP, that seems to have been the culprit any time I've had pieces of logic come up dead-in-the-water. Is there anything else, driven by the Nios, that you can confirm is working (like a flashing LED, or the like)?

I would make sure that the polarities of the resets in your new logic match the naming convention, as well. In the past, I've uncovered problems where the IP generator calls a reset "aclr" by default, when in fact there's a pull-down menu for selecting if you want the reset active-high or active-low, and it doesn't necessarily confirm that the two match.

I also seem to remember my Nios projects having a reset module that's a clearing-house for the entire soft CPU's resets. If there's some handshaking that goes on between your logic and this module that's holding it in reset, that might be the problem, as well.