Update:
Found new temp solution.(see bottom) By replacing different component, even the player, the problem persisted with all possible combination, except temp solution 2. It's not svp, not madvr, not LAV filters, ffshow raw filters, even 3 of them removed, issue still persisted. Must be an issue across multiple filters or even OS + hardware(see below OS/BIOS/Driver replacement).
Control:
Hardware E31230-v2, gtx 960, h77chipset, RMi 650 PSU
Software SVP bundled ffshow,Lav, Mpc hc, madvr
All settings are default, brand new windows 10 OS
Latest driver for the card 361.75.
Issue summary(all videos):
Full screen playback lagged once per second. (Tearing test orange line 'twitching' often)(Exclude overlay-ed full screen and windowed)
Render queue drops, present queue drops to 0.
0-1 drop frames per second, sometimes with color tile artifacts(In the video not shown)
CPU, GPU usage under normal range.
(see https://youtu.be/WlQo4b96Qbw[Uploaded, note that follow the mouse movement are important])
(see log and images)
Possible solutions tried:
OS re-installation
Default settings for SVP4 software.
Direct3D Fullscreen.
Turn off filters except ffshow raw video.
Set Lav to copyback.
Set Lav to none.
Manually set cores to 7.
Disable SVP (Issue persisted)
Disable Madvr (used default output renderer) (Issue persisted)
Use another player (Potplayer Issue persisted)
Windows version update
Installing previous GPU driver version 350.12 and others
Reset BIOS
Replace LAV filters to haali filters
Temporary solution 1:Force overlay video progress bar to stays on top.
[Flawed, audio is not sync]Temporary solution 2:Replace Madvr to haali video renderer
Attached log file/images for help, thank you for reading. All the edit are summarized into the above reading friendly table. Pardon my grammar =].