Ok, if the memory was left at the defaults then it would probably be 1 cycle read latency. So the commands and write data will be pipelined into the memory but the readdata out of the memory will not pipelined.
I dug around my email and found the memory corruption issue. Turns out it only affected DCFIFO at 11.1 (no service pack) so you shouldn't be running into this with the on-chip RAM component.
I would have the hardware team take a look at the timing analysis reports to make sure they don't have failing paths from the on-chip memory over to CPU 2 (or from CPU 2 into the memory). If there are failing paths you could bump the read latency of that memory port to 2 to get some extra pipelining in the readdata path. The TCM connection would need to remain set to a read latency of 1 since that's the only latency Nios II supports with the tightly coupled connections. If the failing paths are into the memory then additional pipelining in the fabric will be needed, I would probably do this with a pipeline bridge so that you don't get pipeline stages all over the place.