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Try doing a memtest and a CPU stress test.

did you try playing games with Gsync disabled?

And, are you saying that there are still frame drops, freezing and micro stutter even if you reduce the graphic settings to low in games?

1. I did memtest. No errors were found. CPU stress test in AIDA64 show good results. Max temp was 72C with 4.7 GHz.
2. Yup. I tried. No changes.
3. Yeah. Even with 1280*720 and minimum settings I notice issue.

=(
 
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Got another SSD you can install the games on other than your OS SSD?

Installing them onto the HDD is never going to help because even with non-gaming activity on the M.2, it will still be faster than the HDD.
Think that's not helpful. I haven't more SSDs. And installing OS on the HDD won't be a great idea.
 
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Actually, having ploughed through the wall of text:

Are you sure the games aren't running borderless instead of full screen?

Also, set vsync to on in Nvidia control panel and off in game.
1. 100% sure that they're running in FS mode. Checked it twice.
2. Tried it. Hopeless. Only GTA 5 game VSync option help a bit but don't destroy FPS drops completely. =(
 
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http://www.resplendence.com/latencymon

Set it running, play for 15 mins, refer back to it to see what's causing your stuttering.
I tried to run it during OS idle. I guess, running during the load it'll showing wrong results because a game remain all hardware power and LatencyMon will performance parasite. LatencyMon while gaming it's like playing game with other 3rd part app running in the background. If wrong — correct me with proofs.
That seems to be an unbelievably low amount of RAM you have there for a modern rig.

Are you able to check how much memory you have whilst you run those games? It may be running short and resorting to using the page file. That can cause chopping too.
Nope. =)
Do you think that 16 GB is not enough for today's requirements? It does not. I have used maximum 9GB of RAM playing one hardware demand game (Witcher 3 if I'm right).
I would try to use in game FPS locks at 140 FPS if possible. If not use DSR to bring them down g-sync isn’t pretty over 141 FPS. Also turn off fair works in Witcher 3.
Not all games have built-in FPS lock. Better to use RTSS for capping frames. Oh, if it would be useful. I tried it, no changes. Even tried to enable GTA's frame scaling to maximum value — didn't help.
About Witcher, I tried to do this. But there was no changes.
I'm really disappointed with these issues on top PC. I don't even know why quality testing is so poor nowadays. :(
 
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UPDATE 1:

Just an hour ago I did:
1. Disconnect my Aorus GTX 1080 Ti physically from the motherboard.
2. Uninstall NVIDIA Driver 391.35 with Display Driver Uninstaller.
3. Switch to the Intel's Integrated Graphics, download and install the latest Intel VGA driver.
4. Lower all GTA 5 graphics settings to minimum and set 800*680 screen resolution.
5. Start playing.

The average performance was about 72 FPS. But drops and frame time spikes still happened at lowest possible graphics settings with 800*680 resolution! I'm really disappointed. Issue didn't go away even WITHOUT GPU and NVIDIA driver.
Then I opened the Latency Monitor and started playing GTA 5 again. After 5 minutes of gameplay I switched to LatencyMon and noticed that highest DPC latency was about 202 ms (instead of normal 30-90 ms) for this driver "Wdf01000.sys - Kernel Mode Driver Framework Runtime, Microsoft Corporation". I think that WIndows 10 is the culprit but not 100% sure.

You can check the MSI Afterburner GTA 5 log.hml available in the Google Drive folder: https://drive.google.com/drive/folders/14DrbFKVLNyiAG4zBtAWWF6soUT91ApyY?usp=sharing
 
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Not sure if it will help but you could enable HPET and force the system timer to be 0.500 milliseconds.

https://forums.guru3d.com/threads/windows-timer-resolution-tool-in-form-of-system-service.376458/

There's also a tool on guru3d that enables devices to use MSI rather than IRQ requests. Test one device at a time with it and make a restore point. I've got it enabled on GPU, Soundcard, sata controller and usb controllers.

https://forums.guru3d.com/threads/windows-line-based-vs-message-signaled-based-interrupts.378044/

Use the V2 tool on the first post.
Thanks, man. Will try it.
 
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And get another SSD to replace the HDD crappiness.

Didn’t realise people still used HDD’s in modern PC’s other than for storing photos or music.
Of course, I do. I use the HDD for storage and not demand games. I tried to play games on both storage devices, no matter. It's affect only loading time, no FPS bonuses from playing on the SSD.
 
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UPDATE 2:

So, I have recently retested GTA 5 performance with the following tweaks:

- Downclock the CPU to 3,700 MHz
- Disable Hyper Threading and Intel VT
- Disable ASUS Multi-core Enhancement
- Disable all the C & P states
- Disable Base Clock & PCI-E Spread Spectrum
- Disable HPET using cmd command and the Device Manager
- Enable Threaded Optimization in NVIDIA Control Panel

I noticed more frametime spikes and long stuttering after applying mentioned tweaks without any FPS lock.
But, with 150 FPS lock there was no drops or any similar issues in GTA 5.

MSI AB Hardware Monitor Logs (with & without FPS lock):
https://drive.google.com/drive/folders/1jmoWxPj0rZ73qYA4noabaeDX_PSw840j?usp=sharing

LatencyMon during game without FPS cap: https://drive.google.com/drive/folders/1gim1F9ypbhXzjr4GxSER56b_rapZBDaO?usp=sharing
 
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So, I recorded new data.
Reverted my BIOS settings to previous, turne ON threaded optimization, set app-controlled refresh rate.
Set GTA 5 graphics to minimum possible with 800*680 resolution and tried to play on GTX 1080 Ti.

Frame time spikes occur again as it was on Intel's GPU with unplugged NVIDIA GPU. The same issues occur less times BUT are more continuously (when start) on 1080 Ti compare with Intel! So weird. Maybe NVIDIA driver adds sticks to the fire.

Here's my hopeless results with NVIDIA GPU: https://drive.google.com/open?id=1_7j8DehnwU5jqfqePZHpa5TMhVcPs8Ul

Logs with Intel's GPU: https://drive.google.com/open?id=14DrbFKVLNyiAG4zBtAWWF6soUT91ApyY
 
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You know at that low of resolution, you are completely CPU bound. You are going to get stuttering on the 1080ti. Just use 1440p to do tests at 1080p or lower you are running into CPU bond situations more often.

Try running your CPU, Case fans and graphic card fans at 100% and play games and see does that help.
1. Oh, really. I've noticed 98-100% CPU utilization when starting GTA 5 on lowest possible graphics settings using Intel's GPU. And even in this scenario I noticed issues and WHAT MORE IMPORTANT in bigger amount! I thought it's the Intel's GPU weakness but now think that is CPU or MoBo related. Well, why at lower graph. sets CPU loads more? Only GPU load should reduce, CPU, maybe, also should have more rest because of less detailed objects geometry. What the reason of high CPU usage when at low settings?
2. Yeah, I tried to max out fan speed. Wasn't helpful.
 
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