Lag issues.

After more and more troubleshooting I'm honestly thinking that it's a motherboard defect, however I'm not pinning it on anything just yet. I'm lead to this as GPU-Z is stating that my card is on a 1.1 x16 slot @ 1.1 x16 when it should be @ 3.0 x16. I also tried other MB PCI-E slots but the same issue was there.

And as for the graphics card, Originally I had an ASUS GTX660, and I had the issue. I RMA'd it and got an MSI GTX660Ti and the problem is still there. However the period I was on HD4000 (and also on basic, not aero) it was flawless.
 
After more and more troubleshooting I'm honestly thinking that it's a motherboard defect, however I'm not pinning it on anything just yet. I'm lead to this as GPU-Z is stating that my card is on a 1.1 x16 slot @ 1.1 x16 when it should be @ 3.0 x16. I also tried other MB PCI-E slots but the same issue was there.

And as for the graphics card, Originally I had an ASUS GTX660, and I had the issue. I RMA'd it and got an MSI GTX660Ti and the problem is still there. However the period I was on HD4000 (and also on basic, not aero) it was flawless.

If your not tired with all the stuff that u have already done (i would definately be) try different copy of windows ? thats just the suggestion. U said its working ok with basic settings without aero so maybe it is really just the windows problem.
 
If it was true and it would work with 3rd gpu hes very unlucky to receive a second card thats causing exactly same problem.

I have had 2 bad GPU's after an RMA, you have to eliminate everything possible when dealing with things like this, no point just presuming that it works is there ?
 
According to windows, and several programs I have run which do HDD defrags and registry effor checks etc. My computer is not powerful enough to support Windows Aero and might stress my CPU.

I'm sorry but, 3570K @ 4.5GHz, GTX660Ti and 16GB of 1600Mhz RAM can't support aero? Hmm.

I seriously think there is a motherboard issue here...

EDIT: Here's a picture of it saying the above in Windows -> http://puu.sh/1X2oC

EDIT 2: Here's a picture of it saying the above in Auslogics Boostspeed (A good & lightweight defrag / registry error checker / system cleaner I have used from a long time) at the top where it mentions Aero Effects -> http://puu.sh/1X2rt
 
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