[Klojum]

When watching movies that require subtitles I use SubScene and have set up Kodi to auto download any subtitles it requires and place them next to the movie.
It doesn't do this.

Do you have the NAS share set up as readonly?

What type of subtitles do you use: SRT or SSA/ASS? Something else?
SRT subtitles have font size tags, so that can be one difference.

All in all, you can change the subtitle font size in the Kodi GUI (not sure if they override sizes inside subtitle files).