Hi, this is actually a bug in Item Popup, not Fast Travel. I will fix this asap, thank you for the bug report. If you want to fix it yourself you can search for alias_CGMZItemPopup_GameParty_gainItem in CGMZ Item Popup's js file and replace the function with this:
const alias_CGMZItemPopup_GameParty_gainItem = Game_Party.prototype.gainItem; Game_Party.prototype.gainItem = function(item, amount, includeEquip) { alias_CGMZItemPopup_GameParty_gainItem.apply(this, arguments); if(item && amount > 0) { const type = (DataManager.isItem(item)) ? "item" : (DataManager.isWeapon(item)) ? "weapon" : (DataManager.isArmor(item)) ? "armor" : "invalid"; const id = item.id; if(this.CGMZItemPopup_shouldPop(id, type)) { $cgmzTemp.addItemPopupToQueue({type: type, id: id}); } } };