I've seen this bug (or one very similar) before as well, I think it predates crepuscular rays revisions as well. I'm running Linux - when the bug occurs the binary spits out an error to my shell window saying something like a "glibc double free error". I'll have to confirm exactly what it says when I have some free time at home.
Also, I think that the cause of the issue to do with the launcher option for 3D shockwaves as the bug has only occurred when this is enabled. I'm speculating a little bit here, but it seems like it occurs when your viewpoint is "hit" by a shockwave, i.e. normal 2D shockwaves are always perpendicular to your viewpoint, so you never get "hit" by them unless you have 3D shockwaves enabled (which makes then spawn in random directions).
Anyhoo - to test my theory, MetalDestroyer - could you confirm if you've got 3D shockwaves enabled in your launcher? If this is the same error I had we should probably mantis it...