Try to learn from here:https://code.google.com/p/pms-exsport/wiki/FAQ
Anyway your priority settings is "it,eng,und".
If embedded subs are correctly tagged, PMS will recognise them as ENG.
If external subs are named exactly as a movie (like moviename.mkv + moviename.srt), PMS recognises them as UND.
If external subs are named in this way: moviename.mkv + moviename.it
.srt, PMS recognises them as IT.
So in your case I suppose first IT is not found but second one ENG is found as embeded and loaded. Third UND (your external subs) is not taken into account.