Last time I checked following while flying (or swimming) did not work well. It's either a bug or an implementation issue with following and the z-axis. You could try using /bug but I wouldn't hold your breath waiting for a fix. I always include a bard in my groups because of the need to travel by land (or group lev over water). If I do need to fly to get somewhere inaccessible (very rare after IoD) I just shuttle them individually.