Edit: adding a timecode fixed the video in the vse, it linesup where it should now when overlayed ontop of the original. I shoulda tried that to begin with. I still want to know what's going on here though. The meta data for avi exported out of blender is messed up according to ffmpeg afterall, something still isn't right.
Note: This has absolutely nothing to do with audio.
fps: 24; no audio codec; h.264/avi/ffmpeg; 100% percent scale; 1080p (I know it says 23.97 in the picture, but I changed it afterthefact to test out decimal fps)
How to recreate: Quite simply I create a series of colour strips in the vse using default settings (making 3 min video or longer). i choose ffmpeg->avi->h.264. Render out with no audio codec. Toss the movie back in....and the colour strips are offset by two frames with the exception of the first colour strip which starts correctly and just ends 2 frames over.
Doing an operation on this video in ffmpeg (even if I'm copying the streams) will display the same message found in the above thread with avi instead of mkv:
[avi @ 0x55be05d8ee20] Timestamps are unset in a packet for stream 0. This is deprecated and will stop working in the future. Fix your code to set the timestamps properly
Testing this on a full video (long 30 minutes) though I see there can be anywhere between 2-4 frame differences at any given point in time.
Recreating with different container? Mp4 works fine. Mkv works fine.
NOw you might be thinking: Well then just use mkv! Well I can't, because I have a different problem with mkv where the meta data for the video goes crazy. It thinks the fps is 1000, on playback its fine and everything is okay. But if I do ANY operation to this video it'll change the offset and playback will jump to some random fps.
Thankfully mkv works fine when I use an integer fps...so I can use it in this case. But I'm really in dire straights here at this point and the only solution I can think of to cover all my bases is export the video in mp4 then convert to mkv in ffmpeg.exe. But for some reason the colouring and quality of mp4 is bad, which makes no sense cause it's just a container! I haven't properly tested if converting to mkv can solve the colour and other quality problems properly, but I will.