Since I started using my Logitech G13 I've been noticing that my BO space skills like to self-change their keybinds. After observing this behaviour for awhile, I've tied it to whenever I train then up by a point or two. This is very annoying because I use the G13 to keybind, and then I go smacking keys that don't work anymore. Now that I know to look for it it's not a big deal, but still, skills shouldn't change keybinds when you train them. Sounds like a bug to me!
I agree, its definitely a bug. However, I don't think its just limited to using any additional keyboards/key pads, etc. I keep my action bar open to all 3 bars, and anytime I upgrade a BO skill, that skill will randomly move to a different open spot on the action bars.
The same thing occurs when I learn a new skill (it will place itself in an empty action bar slot), so I'm guessing that it is treating these upgrades to skills you or your BO already has as if it were a new skill, rather than checking the placement / keybind of the previous version of the skill and using that action bar location or keybind.