DE III problem witch Voltage of the I/O pins

I guess the lower voltage on GPIO probably means you have some design issue in the connections outside fpga. For example another signal is driving gpio or excessive current is being drawn from fpga output.

Are gpios connected to anything?

Can you also check gpio with an oscilloscope? Maybe the signal is not stable, because some switches configurations introduce an abnormal modulation; since the multimeter is slow, it measures the mean value and you simply see a lower voltage.