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});
}
}
};