My latest test with Toolbag 3's vertex color baking is producing some buggy results. I have a scene with three Bakers, one for each of the materials assigned to my low poly model. For one of the three, I get perfect results. The other two produce this weird collection of squares. I did a test in xNormal (no cage) to make sure there was at least some color in my HP file. Comparison below:
(Left - xNormal, Right - Toolbag 3)
This must be a bug considering my first bake was perfect but the other two with identical Baker settings (excluding individual cage / skew paint values) resulted in this. I'd be happy to send off any files for testing.