Will pcie-x16 running @4 will affect nvidia 9500gt 1gb ddr2 card

If the Default clock = 800 MHz and the GPU clock = 400 MHz then try running a Game or other GPU intensive App {e.g. Benchmark} in the background and look at GPU-z again.

Regarding PCIe x4 + nVidia 9500GT, no your GPU cannot saturate x4 lanes, but again try running something 'GPU intensive' and recheck ;)

I personally remove any BIOS 'energy savings' settings and I've seen similar issues with Default BIOS and Default Windows power savings...