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ZFR: Haven't updated in a few months, so I could try it as a last resort. Problem is, if I try it now it would require a system restart, which causes the problem to disappear anyway, so I wouldn't know if it was fixed or not.
Sometimes a clean reinstall of the video drivers can fix all manner of freak issues. Give it a go and if the problem never resurfaces, you'll know it did the trick :).

To be honest a video driver upgrade or downgrade is among the first things I'd try if I had the same issue. I don't think you mentioned the graphics card you're packing, but newer graphics drivers have been known to cause issues with older cards.
Post edited March 07, 2017 by WinterSnowfall
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WinterSnowfall: To be honest a video driver upgrade or downgrade is among the first things I'd try if I had the same issue. I don't think you mentioned the graphics card you're packing, but newer graphics drivers have been know to cause issues with older cards.
I use GeForce 970 GTX. Gigabyte's.

Also, I just tested it, and both GPU stress test and running games on highest settings don't seem to be affected by this. I still get the same results even when the videos stutter.

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WinterSnowfall: To be honest a video driver upgrade or downgrade is among the first things I'd try if I had the same issue.
I'll try a clean install now.
Post edited March 07, 2017 by ZFR
Sounds like your RAM is paging. Do you have sufficient RAM to buffer the video you're watching? We often forget about that these days because everyone has tons of RAM, right? But it could be that you're getting full and dumping to a page file.
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skeletonbow: Try switching from the default video output to specifying it yourself. Choose either DirectX or OpenGL and then restart the player after saving settings. If it still stutters, try the opposite output and restart again.
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ZFR: OK, some progress:

Heavy stuttering when using:
_Direct3D
_DirectX (DirectDraw)

Very light stuttering (but still noticeable, like 1 stutter every few secs) when using:
_OpenGL
_Direct2D

No stutter when using:
_Windows GDI
but... when I open some high resolution videos using Windows GDI I get some colour artefacts on screen. I imagine this is what Windows Media player uses, since it has no stutter on most files, and doesn't open the high resolution videos that produce artefacts when running on VLC.

So... any advice on how to proceed from here?

EDIT:
Not sure I mentioned this before, but using Windows 7, GeForce GTX 970 graphics card.
DirectX diagnostic tool shows no problems.
Yeah, try increasing the size of memory cache/bufferfor video in the advanced settings of VLC, however I can't tell you what it is called exactly as I forget. Basically it reads some off disk, decodes it and plays, then reads more etc. If the buffer runs out faster than the disk replenishes it you'll get jitter. Increase the buffer size uses more RAM but should be smoother. Might need to hit up Google or Youtube for the setting though as it's been a while since I twiddled with that stuff.
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paladin181: Sounds like your RAM is paging. Do you have sufficient RAM to buffer the video you're watching?
32 GB...
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paladin181: Sounds like your RAM is paging. Do you have sufficient RAM to buffer the video you're watching?
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ZFR: 32 GB...
Do you have the 64 bit version?

It really does sound like a RAM issue (or something similar) but there really shouldn't be a way it's possible with that much RAM...
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ZFR: 32 GB...
Well, then that's not the problem. Sounds like the problem, but not with 32 GB... I'm sure you reinstalled your GPU drivers?
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ZFR: 32 GB...
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adaliabooks: Do you have the 64 bit version?
Yes.
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ZFR: 32 GB...
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paladin181: Well, then that's not the problem. Sounds like the problem, but not with 32 GB... I'm sure you reinstalled your GPU drivers?
Yes.

Waiting to see if it appears again.
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adaliabooks: It really does sound like a RAM issue (or something similar) but there really shouldn't be a way it's possible with that much RAM...
Also, I did memtest on my RAM few weeks ago, and no issues came up.

And, as I've written, games still run at more or less same fps when the issue occurs.
Post edited March 07, 2017 by ZFR
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skeletonbow: Increase the buffer size uses more RAM but should be smoother. Might need to hit up Google or Youtube for the setting though as it's been a while since I twiddled with that stuff.
Sorry, just noticed this post. If those are the "cache" sizes, then I played around with them and there was no change (other than making it much worse when I made the size extremely small).
I had this problem with VLC on my pc a few years back and for some reason I tried everything and nothing worked so I switched to mpc hc and my god man never turned back I love this version way more.

You should give it a shot and prob ditch VLC to try something new?
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UnrealQuakie: I had this problem with VLC on my pc a few years back and for some reason I tried everything and nothing worked so I switched to mpc hc and my god man never turned back I love this version way more.

You should give it a shot and prob ditch VLC to try something new?
I probably will switch to MPC HC if nothing else works, but seeing how it's not just a problem with a single program (also happens on Pot Player) and on MPC HC when choosing "System Default" as output, I'd rather figure out what exactly is causing this.
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UnrealQuakie: I had this problem with VLC on my pc a few years back and for some reason I tried everything and nothing worked so I switched to mpc hc and my god man never turned back I love this version way more.

You should give it a shot and prob ditch VLC to try something new?
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ZFR: I probably will switch to MPC HC if nothing else works, but seeing how it's not just a problem with a single program (also happens on Pot Player) and on MPC HC when choosing "System Default" as output, I'd rather figure out what exactly is causing this.
I tried for weeks when I had the issue and looked and talked on forums about this and some say external audio or built in audio on motherboards are the cause of it but I don't believe that. I wish you luck man but do consider mpc, I feel they polished the program to work with many hardware combinations.
Try an older version of VLC? I'm using 2.0.7 and no issues myself. MPC works too.

Do you have CCCP installed? (Combined Community Codec Pack), I think the last version was from 2014, but I've never had issues when relying on those.
Install Sysinternals Process Explorer for free from Microsoft (hit up google), and you can examine the advanced process listings for clues about I/O and other stuff in the advanced column configuration that could lead to clues about why performance is problematic etc.
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rtcvb32: Try an older version of VLC?
Tried that already. Didnt work.

The reason I dont think its codecs is because it's andom. And happens with all files when it does regardless of codecs used by the file.

I reinstalled graphics drivers waiting to see if it appears again.

Also uninstalled 2 utilities that came with the motherboard. Smart recovery and smart time something. They were the only 2 processes running that I didnt recognize. Im generally careful not to have any bloatware installed and I am not experiencing any other issues anywhere else. I'll see how it goes.