Negative Setup Slack time

Ah this is making more sense now. That node with the -2.374 slack is an open core plus node which is known to cause the behavior you are seeing. I'm guessing you either don't have a license for the Nios II core or the SDRAM controller. Since -2.374 is a lot of negative slack the fitter is probably trying to optimize that path to the point where it's not focusing on optimizing setup times. Try cutting that path above using wildcards and recompiling to see if your setup slack issues go away. You'll need wildcards since most of the characters in that instance name are randomized.