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Problem with stutters, graphics card?

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Hi, I have a problem with my computer "lagging" or stuttering (if that is the appropriate description for the issue) every 1 second once I run a html5 game on the internet. The game basically is smooth then locks stutters for some miliseconds, then is smooth once again. it is quite regular just as a hearbeat.
Additionaly when running html5 content, I hover my mouse over an icon and wait for a help bubble to apear, the game lags some more.
As you can imagine that creates a poor experience but I am more worried about the stutter every second issue.
Now basically I am venturing into html5 game design that is why I need this solved.
Plus it is ridiculous that such an expensive rig cant run simple html5 web content smoothly without problems.

I have tried searching for the solution for a week now with no luck.

I have done the following to try and solve the issue:

1) Formated the computer.
2) Installed new fresh Windows 7 64 bit.
3) Installed all the up-to-date drivers for all the components, including graphics card.
4) Updated bios.

Once this did not help I installed all the updates for Windows 64 bit, which took about 3 hours to install, and still that did not help.
(Just in case anyone was wondering, yes I have an original Windows copy.)

So basically I have a freshly installed system now and still I am having problems.

My computer specs:
Stationary Workstation (not laptop)
Windows 7 - 64 bit
16 gb ram
NVIDIA Geforce GTX 960
Dual Intel Xeon E5-2697 @ 2.60 mgz each.
ASUS Z10PE-D8 WS motherboard
2 GB hard-drive (I cant remember the model, altough its not too fast)
My monitor has a refresh rate of 59 Hz

I have tried to run html content on Firefox (the worst performance), Opera and Chrome.
I have tried turning off hardware acceleration in all the browsers.

I did not know what to do so I tried to mess with different resolutions and ran a small program in debug mode and this is the outcome:
Resolution: 1280x800 px -----> 37-39 FPS in debug mode - very choppy
Resolution: 1440x900 px -----> 60 FPS in debug mode - No lag, seems that Im on to something (but I dont want to work or view the game in this resolution as its blurry)
Resolution: 1680x1050 px ---> 58-59 FPS in debug mode - Overall smooth, every time 1 second mark is passed there is a jitter/quick lag
Resolution: 1920x1200 px ---> 59 FPS in debug mode - Overall smooth, every time 1 second mark is passed there is a jitter/quick lag (same as above), really really annoying!

It seems that at a smaller resolution the stutter went away. But I dont want to work on a different resolution.

Now I have switched monitors to see if it was the monitors fault. The second monitor is a 59 Hz too but a 1600x1050 and still the stutter remain, while at 1280x800 it sometimes is and sometimes isnt.

I have been reading about vsync issues, I have had tearing in the past on this computer but did not know what that was or how to fix it. Still I cant seem to do anything.
This stutter issue does not seem to be the tearing due to vsync that I have been reading about, but Im not sure to be honest. As I said it happens every second like clockwork on the higher resolutions.

I have read that it may be a driver problem? Altough I do not have any visible driver problems in the device manager under control panel.
Ive also read that it might be a hardware problem?

Any help would be appreciated, I really dont know where to go from here.

Thank you for any and every help.

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Get Process Explorer
Save it to your desktop then run it (Vista or Win7 - right click and Run As Administrator).  
View, Select Column, check Verified Signer, OK
Options, Verify Image Signatures
Click twice on the CPU column header  to sort things by CPU usage with the big hitters at the top.  
Close all browsers
Wait a full minute then:
File, Save As, Save.  Open the file Procexp.txt on your desktop and copy and paste the text to a reply.
Get the free version of Speccy:
http://www.filehippo...download_speccy (Look in the upper right for the Download
Latest Version button  - Do NOT press the large Start Download button on the upper left!)  Download, Save and Install it.  
Repeat creating a log but first fire up your game and wait a minute.
While the game is running and you are getting your stutter look and see if a program jumps to the top about the time of the stutter.  Often this will be wmiprvse.exe or your antivirus.
Close all browsers and open programs before running Speccy.  Run Speccy.  When it finishes (the little icon in the bottom left will stop moving), File, Save as Text File,  (to your desktop) note the name it gives. OK.  Open the file in notepad and delete the line that gives the serial number of your Operating System.  (It will be near the top about 10 lines down if they are still putting it in.)  Save the file and close notepad  Attach the file to your next post as it is usually too large for the forum plus it will maintain the formatting and make it easier for me to read. (Click on More Reply Options then Choose file, select the file, Open, Attach this File) Uninstall Speccy.

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