So, I've been trying to fix it myself for quite a while now and no success.
It only happens when GPU accel is turned on and it happens randomly when I stroke, sometimes it goes smoothly and sometimes it skips start and/or end of the stroking and renders the full stroke after normally.

With GPU acceleration on:
https://i.imgur.com/Va5z6KT.gifv

Without:
https://i.imgur.com/khqc5uA.gifv

Everything works normally on Gimp, Sai, Sai2 and Clip Studio, so I'm pretty sure it's Krita specific.
I've tried disabling/enabling smoothing, disable/enable instant preview, all presets, updating video drivers, close all other softwares.

Setting CPU affinity to just ONE core actually made the issue far more apparent, so I guess it's multicore related issue?
https://i.imgur.com/MjIkpRd.gifv

I got a Wacon Cintiq 13HD, 8G DDR3 (dual-channel), Nvidia Gtx 970, I5 processor. (Windows 10)

Thanks in advance!

Sounds like the instant preview (which is a feature), try turning it off

https://docs.krita.org/Instant_Preview

Well, I did say I tried disable and enable instant preview, I guess I forgot to say I tested doing it on both per preset and the shift + L thing.

There's still 4 other things it could be:
1. High bit depth image(so higher than 8bit).
2. Some windows accesibility feature that turns long presses into right click(though sai would be affected by that too)
3. Touch support interfering? You can turn this off in settings->general.
4. openGL doesn't quite work, maybe switching to angle?

1. Nothing changed
2. Exactly, sai would be affected aswell so nope
3. Nothing changed
4. Already tested Angle, nothing changed either.

I just realized it also happens with the mouse, the hiccups while stroking.
Is there any advanced openg settings I could play around with?