Your problem is probably a CPU bottleneck. At your resolution the GTX 560 is hard pressed to use its full capabilities. It's really a card more appropriate for 1080p. Open task manager and keep it running in the background while you play, monitor your CPU usage. If all 4 cores are hitting 100% that means your CPU is working at its maximum, and your graphics card has to wait for the CPU to catch up, hence the lower performance scores.
AMD's Phenom II processors while still viable as gaming CPUs, are starting to show their age. They are competitive against the old Core 2 CPUs from intel. They can't hold a candle to intel's current CPUs though, especially if you are trying to game at a low resolution like 1280x1024. If your CPU usage is at 100%, all you can do is try to overclock your CPU higher. The other option is to get a higher resolution monitor, which would push most of the workload back to the GPU.