Have exactly the same problem!
Please, there some way to fix it?
I want PS3 Media Server to load by default the external SRT subtitle instead of the embeded subs in the MKV. On the last version of PS3MS all worked perfect, but now on 1.72 it loads the embeded sub always.
I found the solution, use the folder TRANSCODER and select the option of the Undetermined Sub, but I want it to do it by default like on older versions.