Using Altera Nios II Stratix II dev kit just as FPGA.

Hello.

Got this board without any intention to use Nios, but just to use
EP2S60 chip.
Drawed very simple schematics, loaded it via EPCS config port (using
Active Serial Programming method), powered it, and all LEDs are
blinking, with about 2Hz frequency, except of those LEDs which was used
in project. However, when one of LEDs must be turned on regarding my
goal, it blinking modulated by about 2Hz.
What is this? Probably some problem signalization, but where should I
start?