Subtitle problem in Mediacoder.

I am naming my subtitle file with the same name as the videofile and adding it in the mediacoder options. Still I get no subtitle when transcoded.
Is there something else that must be done?

Not sure how much help it is to you, but some encoders only understand certain specific subtitle files.

For example, the mz video converter included with my miniplayer, only understands .srt files.

I had to find some srt files from a website that hosts subtitle files, and then everything went swimmingly.

I had to tweak things a bit more, but its a start for you to make sure the encoder you wish to use supports the subtitle extension you have with your video.