keyboard are block at payment time in POS . So You need to override both

this.keyboard_handler = function(event){
var key = '';
            if (event.type === "keypress") {
                if($(".your popup div class").not('.oe_hidden').length){
                    return;
                }

              rest of code......
};

and 

this.keyboard_keydown_handler = function(event){
            if($(".your popup div class").not('.oe_hidden').length){
                return;
            }
     rest of code......
};

Thanks