yeah, you have to kinda watch it if a video you intend to import has letterboxing already in it. You might have to take that video, and crop it in an external video editor like Magix Movie Edit Pro, or Pinnacle, or Avid, or whatever you have with that capability before importing into iClone.
Now, as far as the video appearing "transparent"...first, of course, make sure you check your opacity settings (usually found as a slider somewhat below the Material Textures and Settings boxes). Also, you might simply need to turn the plane (or whatever surface you are superimposing onto) around 180 degrees opposite of its current facing, unless it means turning around the entire prop, then you might wanna hold off on that, but there's still at least one more option.
You'll notice three little color boxes further down the Material Textures and Settings side...the three boxes are Diffuse, Ambient, and Spectral. Try turning those to solid white, and see if that solidifies your video at all. :)
Hope these hints help. :)
"Incompetence will always prevail so long as evil men stand by and do nothing."
-Martok2112