I'm not sure if this will help the OP or not, but I was messing with this for quite a while and I think I found a solution.
I was experiencing the semi-transparent subtitles when viewing DVD iso rips. Here's my solution. Edit the mEncoder Expert Settings : Codecs specific parameters and enter this:
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container == iso :: -vf-add format=i420,scale,expand=-1:-1:-1:-1:1,format=bgr24,scale
What that does is enable an extra set of options that only takes effect when viewing DVD isos. You may want to specify "true ::" or maybe "container == vob ::" instead, depending on what you're viewing.
Here's why it works (I think
The OSD in mencoder doesn't work very well in the color space that DVDs are in (yv12) as described here: http://lists.mplayerhq.hu/pipermail/mpl ... 40805.html
My solution was to use the video filters to convert to bgr24 colorspace, apply the overlay with the "expand" filter, then convert back to a color space that the mpeg2video encoder likes (i420)