Ugh, ok I have seen a problem with the hotbars and keybinds.

When you set a keybind that already belongs to something else..the nice little warning isn't telling you that it will be unbound from another location.
It is telling you that it will ALSO be bound to that same hotkey...
The only way I have found to fix that is to find the key in the options and disable it first, then bind it to the hot bar.

BUT..I haven't been able to get a CTR+Shift+# key to not swap banks on my hotbars...even after deleting the keys. :S