Just following up from my initial 2010 post. There have been no brain injuries or anything, and I think the point about shadow boxing without full speed is a good one, as my original theory is still simply that I did not have enough control of my punches to prevent rattling the brain, for whatever reason, which could include A) poor technique, B) weak neck, C) poor flexibility in the back/shoulder/neck and/or D) brain injury or predisposition towards such, or E) a combination of multiple factors.
I would venture a guess that anyone throwing full speed punches (never fully extending but keeping a slight bend) might struggle with this.
I would also like to point out what I think is the benefit to training in such a way. Bags are amazing, yes, but we don't always have bags, and a bag isn't necessarily very similar to hitting a human face with bare fist, so training simply with a "jolt" at the end of the punch can perhaps be a great training tool for practicing bare knuckle fight simulation.