This is happened on smplayer with mpv as default player engine. I have try mplayer and it works perfectly.
When I try video with checked function "Run Mplayer/mpv on it's own window" both mplayer and mpv work perfect if I play directly from mpv/mplayer window. But when I try with unchecked function "Run Mplayer/mpv on it's own window" and make mpv as default engine, Smplayer sometime can't decide what chapter is being played and back to random position of track. I have try in several video which has chapter embedded on it and have the same problem. Can you solve this problem?