I don't actually have access to the repo but I thought I'd post a bug fix:
Apparently the way the animation was iterating over the vertices to add the bone weights, it was overrunning its bounds. If you do the math - if you keep the index buffer and weight buffer in the loop, it would skip to the "next four weights" for each weight access. This seems counterintuitive. If you have a variable called "fourminusmaxweights" then I'd assume you'd want to do that after accessing all weights in that block. I moved it out of the loop and all my multiple weight per vertex animations worked.
Thanks for looking this over and possibly committing it!
--- MeshAnimationController.java (revision 4531)
+++ MeshAnimationController.java (working copy)
@@ -364,9 +364,11 @@
// resultNorm.y += temp.y * weight;
// resultNorm.z += temp.z * weight;
// overwrite vertex with transformed pos