Good day everone! This is my first post

I have a standalone Sony S480 BDplayer that plays many video formats like mkv, it plays smooth except when skipping chapters, but this issue is resolve when i re-encode the video with Handbrake or Mux it into Mp4, but i don't want to re-encode a 6gb file, it would take forever! and i don't want mux it into Mp4 for my Bdplayer can't read internal subs in it nor show external subs (with same filename of video).
The problem with skipping chapters in Mkv is whenever i press the next on the remote the movie won't go to the next chapter, rather in starts again on the current chapter, ?? wth happen? and also to be able to chapter skip, i have to wait like 10 seconds before i press next, then the movie will proceed to the next chapter.
This could be a problem about inaccurate seek time? I don't know what to call this issue.
Please help, it's been bugging me for many months now, i can't find answer on google or other video forums (videohelp and doom9, detect my ip as spammer).
Thank u in advance!
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AMD Athlon X3 440 3.0 ghz
RAM DDR2 3gb
MSI M68M-S2P
ATI Sahppire Radeon 4650 1024gb