Apple Media Tool does not handle transparency well when changing color depths. Here are some recommendations on how you can avoid the problem:
* Keep it Simple. Stick to white or black as a transparent color. Never use 16- or 24-bit transparent colors.
* Do as much as possible with QuickTime background stills. QuickTime does a good job of dithering images down to 256 color palettes on Macintosh and Window computers.
* Use Equilibrium's DeBabelizer Toolbox software to create superpalettes that play on Macintosh and Window computers, then make a QuickTime Pict from the result.
* Test extensively on both Macintosh and Window computers using a wide variety of video boards.