Frame Stuttering in SP mode

Hello all I'm fairly new here (a few hours or so C_C) lol, but anyway I just installed CF and started playing through the SP but I'm having an extremely annoying issue, my game seems to have the micro stuttering issue I don't know why but it is. It happens just about every second or so while out in space and especially when fighting which is where its Really! annoying. If anyone knows how to fix that I'd appreciate it.

Ooh an before I forget here's my system spec''s

Phenom II X4 955BE @ 3.7GHz
4GBs of G.Skill ECO 1600MHz CAS 7
GigaByte HD4890OC 1GB
Seagate 750 SATA HDD (7,200RPM)
ASRock 990FX Extreme 4 MB (Nice MB OMG!)
Zalman CNPS10X Performa CPU cooler with 2 120mm fans
Xigmetek Utgard window sided case
6 AeroCool Shark 120mm Blue Edition case fans (2 on the CPU)
2 AeroCool Shark 140mm Black Edition case fans
Antec 750Watt PSU
LiteOn DVD/CD combo burner ;/

Ok I think I figured out what the issue was and it does have to do with the shaders, now that I know Not to let CF auto patch the game runs great lol, also leaving the shaders on the default *activated* seems to completely remove the stuttering issue. So my issue is resolved, Thank you for your time