Shifted clock signal when connecting to FPGA (cyclone iii)

So I have scoped out several I/O and dedicated CLK pins on my board. I've noticed that just looking at a pin I see a DC voltage of around 1.12 Volts. Is it possible that my FPGA is damaged? This to me seems like I'm seeing the VCCINT voltage (1.2V) with a small voltage drop. I'm not familiar with the architecture internal to the FPGA but to me this looks like the control circuitry could be fried and now I'm just seeing the internal power being applied at the I/O pins. This is definitely the shift I'm seeing in my clock line as well.