I think the problem may perhaps be caused by the option "Remember movie settings". I've done some testing. As long as I hadn't selected this option: no problem. But when used and once "Show subtitles" being selected for secondary subs, this is registered by "Remember settings". However, it apparently doesn't register (for secondary subs) if "Show subtitles" is
deselected by the user after that. (Irrespective of old or new subtitle engine being used.)
(Also this most likely concerns an imperfection in new coding which was added following this bug report http://forum.bsplayer.com/bug-reports-codecs/11589-confirmed-2-language-subtitles-show-fine-but-not-saved-after-closing-bsplayer.html#post42482)