It is in latest SubJunk build but not in official one for now.
Anyway it doesn't work as you described.
Please check this FAQ:http://code.google.com/p/pms-exsport/wiki/FAQ
The logic is described here but it is little bit outdated because new patch included some settings in GUI so not needed to be done manually in config files.
But I think you will understand the logic.
Also you promised to post MediaInfo output where we can see how you tagged subtitle tracks(if it is correct) or are your subs external? All your questions should answer this FAQ link.