HandBrake will convert closed captions and subtitle tracks to ASS format.
The behavior is "intentional", but undesirable.
https://forum.handbrake.fr/viewtopic.php?f=6&t=34522&p=161536
Issue is tracked here.
HandBrake/HandBrake#160
As workaround run handbrake with no subtitles in output, and then remux subtitles back in.