So I'm getting around 50 fps on the following hardware:

Win7 x64
Phenom ii x4 965 BE @ 3.6ghz
GTX 960 2gb Super Jetstream (newest drivers)
8gb DDR3

This is way above the recommended settings but I can't keep up with 60 fps. What's even more suspicious is that I get the same exact framerate whether I set 800x600 low settings or my native 1680x1050 at high settings. Not a single frame of difference.

I know 50 fps is more than enough for a smooth experience but I feel I should be getting at least twice that on my rig.

Any idea what's causing the issue? For the record, I turn all background programs (including antivirus) off before playing so it's not any background process.

Did you turn "Übersampling" off?
it's the only reason I can think of excepting problems with mods.

Yeah, ubersampling is usually the framerate killer for this game, but if you tried low settings already it should have been turned off. The fact that you have 50 fps no matter what you do seems odd, and makes me wonder if you have the framerate locked somehow. Check that your graphics card settings aren't forcing vsync or anything weird like that.

Whether that is smooth or not is up to you, don't rely on it as a standard that it should be.

As for your issue, you likely have some framelimiter which are very useful as long as you choose the right framerate you want.

Have you checked so your monitor isn't set to 50Hz and then the game runs with VSync, that would force it to be 50FPS all the time.