If you can see -- for example -- ^E when pressing CTRL-E, then the control codes are received by the shell/terminal, therefore keyboard related things are not to blame.
Well yes this works.
If so check the shell init files for remapping the keycodes. Maybe revdep rebuild will show a library, which is used by the shell was updated but the shell was not rebuild. Or something like that.
Ok, looking after that, thanks for the input.