Maybe the Video_ts to Mpeg converter can help you solve your problem. Go to dvd-creators.net to find the video_ts converter tool learn more about it. It allows you import plug-in subtitle for your favorite movies. You can also add subtitle from "Edit" opption.
When I try to convert a Video_TS file with subtitles to Mpeg4 with VisualHub, so that it is transfered to my Apple TV as well, I loose the subtitles in the Mpeg4 format. Any idea how to solve this problem?