Following video shows that in mm3d, boolean operations doesn't work so well, but it don't work especially for lengthy objects. Both subtracted objects are the same except one is longer.
MM3D model: http://www.sendspace.com/file/ukcyjp
MM3D rev 440, but it behave same in older versions too.
Related forum discussion: http://misfitcode.com/bb/viewtopic.php?p=485