Cyclone III configuration corrupts image

nCE was reworked from 300 to 10K, from "Cyclone II device family pin connection guidelines PCG-01003-1.1" - and using 10K actually makes it work a little better.

INIT_DONE is enabled. So is CRC. (note what I said earlier) Interestingly, INIT_DONE doesn't seem to work when programming via JTAG, but once the image is burned into EPCS, it does.

How do I know the image is corrupt? 1. The CRC light is on. 2. LEDs that are supposed to be off are on. 3. We can't talk to the NIOS inside the chip.

So, the issue of the day is: what kind of problem would go away when we raise the voltage from 2.5 to 3.3?