For me using my own package the default TTF font used is the font that the symlink /usr/share/mplayer/subfont.ttf
points to - om my PC that is
/usr/share/mplayer/subfont.ttf -> /usr/X11R6/lib/X11/fonts/TTF/DejaVuSans.ttf
I can influence the font that is used on screen in two ways: by setting another font in gmplayer's preferences dialog, in the 'fonts' tab; or else by creating a symlink in my homedirectory called ~/.mplayer/subfont.ttf that points to a truetype font. In my homedirectory I let it point to for instance
/home/eha/.mplayer/subfont.ttf -> /usr/X11/lib/fonts/TTF/aakar-medium.ttf
and indeed, in both cases I get to see that the new font is used for the subtitles when I restart the movie.
So, I don't know what is wrong in your setup but I would check out old configuration files.