Cyclone III slave (PS) embedded memory errors

I think I've found the problem.

There is a trace connected to pin 76 on the master and pin 99 on the slave. Trace is pulled up to 3.3V via 2.2k

This **bleep** resistor was dead, and the trace was actually floating.

I didn't use this pins before, so I can't reveal the resistor is dead.

As I start to use it, all logic became a total mess. Something worked, something not. By elimination I found the culprit.

I can't explain how this trace connected with loading errors (when FPGA not even in user mode), but the fact is - replacing resistor solved all problems, ROMs working now (though I don't use them anymore).

Thanks to all, problem solved!