There are SVQ3 files that ffmpeg cannot decode yet, the ones iam speaking of contain a image or watermark, often a logo in a global header (extradata in ffmpeg, QT has its own funky terminology for it). The binary decoder displays this watermark over the actually decoded video.
FFmpeg is in principle fully capable to decode these videos (and of course without these watermarks), the only problem is that 32bit of the header and following bitstream are modified by xoring them with a per file constant. Our problem is we do not know how the binary decoder calculates this constant. A example SVQ3 video and the corresponding constant of 0xA2A2A2A2 for this file as well as a bugreport on our tracker exist as well
The puzzle is to figure out how the binary decoder finds the constant, its likely not very hard for one knowing how to use a debugger, hint: memory breakpoint at the input data and a cup of coffee or tea or a can with cola.