Question about Cyclone III initialization

Hi,

I am using a Cyclone III part, and I am programming the part through a Passive Serial configuration. I pulse nConfig pin and wait for the nStatus pin to pulse as well. This works consistently, but every now and then, about 20-30 reboots, I never get nStatus to go high, the nConfig is pulsed as usual all times.

Is this a known issue? Any help would be greatly appreciated.

Thanks!