You can try this patch.
(function(alias){ Window_NameEdit.prototype.toggleInputMode = function(){ alias.apply(this, arguments); if(Window_NameEdit._inputMode){ this.$y = this.y; this.y = (Graphics.boxHeight - this.height) / 2; }else{ this.y = this.$y || this.y; } }; })(Window_NameEdit.prototype.toggleInputMode);