Try to set the downloads folder for subs from "with video" to a folder on your sd card. I made a folder "subs" and set this on in settings as standard save point for the subs. This workaround works for me, since a solution is coming.
Thanks! I thought of it.. I also thought that if the subtitles go into a different shared folder that the folder where the video file is located it would work but it doesn't.
I've been testing Emby (I thought maybe it would be different) but with the emby addon set to "native" same exact bug with external subtitles.
I guess I'll have to move all the subtitles out of the shares for now.