Cyclone III configuration problems

I was recently put on a project at my work and they are using an EP3C5F256C6N. We have been having problems configuring the FPGA with AS mode. I've looked at the diagram in the cyclone III handbook and our connections between the FPGA and EPCS4 look correct. Recently I found out that our Vcca was connected to 3.3V instead of 2.5V. I was wondering, before we make a new PCB, if having too high of a voltage would keep nSTATUS low or if something else is causing the problem.

Hopefully that makes sense.

Thanks