You are talking about FORCED subtitles. If you will use same name for SUB as video file has[when using external SRT or SUB], then you will see UND [undefined] subtitles in #TRANSCODE# folder.
When you will use same name for subtitles as movie but ADD e.g. ".EN" or ".ENG", then you will see also LANG name for that instead of UND info.
So an example:
- you have video file Star.Trek.Part1.avi
- you have 2 subtitle SRT files, one FULL and one FORCED with names:
__________under #TRANSCODE# folder you will see it as UND subtitles
__________under #TRANSCODE# folder you will see it as ENGLISH subtitles
So now you can rename your subtitles same way...you can use FORCED subtitleas with ".EN" addon and for full subtitles you can use exact name as video name => then you will find FORCED subs as ENGLISH ones and also in case you set some audio/subtitles priorities, subtitles can be loaded automatically depending on your preference...
EDIT: change AVI extension to your MKV one
If you have embeded subtitles directly in the MKV file then you need to choose corect subtitles manually.....in case that forced subtitles are present