You could check if this is EIA-608 subtitles. MKVToolNix apparently doesn’t see those correct and in consequence won’t offer you an option to drop them. You can however drop them using ffmpeg (native version or the one bundled within your PMS):
./Plex\ Transcoder -i "<INPUT_FILE>" -codec copy -bsf:v "filter_units=remove_types=6" "<OUTPUT_FILE>"
Where <INPUT_FILE> and <OUTPUT_FILE> are the full paths of the respective source/output files.
