I would start with the following:
Open preferences/ controller manager
On the right handside under device setup ‘open’ the traktor s4 default file/tsi.
If you never modified it it should be empty anyway. If that’s the case, delete it (edit/delete).
Then re-import it (add/traktor s4/default).
Check the in port is set to Kontrol s4.
If your tsi default file has commands in the 1st place (you modified it) check that they’re no additional commands added to your buttons that would have the override option box ticked. If that’s the case, remove them (or untick the box).
The really strange thing is that the default mapping shouldn’t be touched by any other tsi MIDI file (as it doesn’t use midi). Are you sure you’re not in midi mode?