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I'm using MKV, although I tried MP4 to see if the chapters were present there, but no dice. And yes, I have chapters selected in the Handbrake presets.

Thank you for the quick response. I'm using the current VLC player and Windows 7/10. I usually leave in English subtitles (not sure what PGS refers to).
If I de-select all the subtitles, do you think that might solve the problem?

Hello. I am a long-time MakeMKV user with a long-time problem that I still haven't resolved -- large file sizes. I have tried to use Handbrake, which runs fine without errors but produces files with no chapters, so in the resulting file I can't even hit "pause", only "stop", whic...