Getting low fps with a GTX560 in many games (but not all)

I've got a PC which I personally picked piece by piece (though didn't assemble myself) which should be more than capable of great FPS in pretty much all games. Even if not 60 on everything Ultra more than 40 fps in mediumish settings should be normal, as far as I know. However, that hasn't been the case. Although many games (i.e. Skyrim, Starcraft 2, Oblivion, Portal 2, Terraria, Bastions) have been running awfully well, as in at least 59-60 fps (vsync on) with no stuttering or lag but some others have been really disappointing. For example Planetside 2, Forge, (not sure) Borderlands and Smite have been running at 30 to 2 fps. Yeah, 2... Smite, the moba game Smite, runs at 2 fps. Now ain't that sad. Though for that game I can say this, in the 1v1 tutorial map, it runs at 60 capped (vsync) with no problem. Here are the specs. Hopefully someone here knows a reason why this happens. I've researched a lot and asked a few friends who are very knowledgeble on the subject and am yet to fix the problem.

OS: Microsoft Windows 7 Home Premium 64-bit SP1
CPU: Intel Core i7 2600k 3.40 GHz, not overcloaked, Currently at 51 degrees celcius.
RAM: 3 x 4 GB 1600 ram and 1 x 4GB 1333 (overcloaked at 1600) ram. (Yeah, bought a lower speed ram and was lazy :P) (Currently Speccy believes they are at 803MHz)
Motherboard: ASUSTeK P8Z68-V LX (LGA1155)
Graphics: 1023MB Geforce GTX 560 (Currently at 40 degrees celcius)
Drives: 2 x 1TB SATA + 1 x 0.5 TB Sata + 1 x 100GB SSD Corsair Force 3
1080p 70 hertz monitor.
Also, Speccy believe the SSD is 128 degrees celcius which I am not sure whether or not is relevant.

Thanks already, I will try to be as cooperative as possible :)
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More about getting gtx560 games
  1. do you msi afterburner? Check that out how much ram you are using in those games. that could be a ram bottleneck.
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