I noticed you only use the tip if your right thumb to press the key, but use the whole left thumb to press the key.
yea, all my bad habits are showing through now that I am used to the matrix layout of the ergodox - you probably noticed that I don't rest on the home row either, and just on the F and J scoops, and I don't always press pinky column keys with the pinky. I actually did do all the correct finger pressings to its corresponding columns when I first began to use the ergodox, but I have no idea what happened in between.
The thumb thing has a lot to do with how the keyboards are positioned in relation to my body and the angle it is tilted at. I just do what feels comfortable and that was apparently it. I really do use the backspace (left thumb) and space (right thumb) the way you pointed out in regular use.