Not likely what you want to hear at this point and, most likely, entirely undiagnosable and unfixable. But, just for the sake of completeness...
MJ occasionally locks up my system during playback; completely locks, such that use of the power switch is required. The exact timing of it appears to be a fairly random distribution. On average, I get this 1-2 hours into use, though certainly not every time. A little experimentation has shown that it is not MJ itself (I can leave MJ playing all day if I'm not actively using my computer, and it never suffers any problems). I've noted two programs that I have been using when it does lock up: Internet Explorer and Gamespy Arcade. I'd completely write off the Gamespy problem as an issue with their notoriously difficult software, but IE seems a bit suspect. Also, I don't experience problems such as these when not using MJ. Again, I fully recognize that a release is impending and don't expect that this can be addressed, but I just thought I'd throw it out there.
As a second, possibly more fixable issue...
The gradient settings for the Super Scope visualization do not appear to function correctly. First noticed this with the Rainbow Cycle setting; it seems to fade to black periodically, but not periodic with the actual cycling of the colors. If you consider three major colors in the cycle (Green, Red, Blue), it will appear every fourth color (i.e. I see Green, Red, Blue, Green, Fade to black, Blue, Green, Red, Blue, Fade to Black, Red, Blue, Green, Red, Fade to Black, etc.). Playing more with it, I noticed other problems with the gradient setting. Setting it just to 0xFF0000 (pure red, in theory), results in a pure blue image (no fading to black). Setting the blob oscilloscope to this same value results in pure red. Green works correctly (0x00FF00), and of course theoretical blue shows up as red (0x0000FF).
Thanks for all the hard work,
Matt