Poncho I have experienced this issue with and without ALiVE. Something to do with landing radius I think. They can't find a suitable LZ, so the waypoint breaks. Then it eventually times out and they head home. I have tested this for countless hours over the last few weeks, and don't have a good fix on what's causing it. Possibly ACE, but that's not proven. Seems worse on Tanoa. Do a test WITHOUT alive (but with ACE). Just give a big helicopter an open LZ and see if they do it. In my testing they'll hover about 90m away if they can't land, or they'll try landing in like 10 different spots like a dog finding a place to lie down. Then do the same with the little bird. Little bird lands.
As far as fixing it, i don't have a foolproof solution but... I make sure no AI mods are on, including turning off as many of the ACE AI features as I can, then I basically give my logcom exact instructions. I make a very high priority objective right next to the logcom module, and I make sure there are both Paradrop markers and helipads in the vicinity. I also make sure I place units around it that are fixed, so the area is always "occupied", as far as the OPCOM is concerned. This works maybe 70% of the time, but it's not a true fix.
Again I think this issue spreads beyond ALiVE. It's particularly bad for medium transports and above, and on newer more cluttered maps like Tanoa. So avoid that stuff? Lol. Every time I bring it up people tell me I'm doing something wrong with waypoints and it works for them, etc... But after so many hours and testing different ways I'm pretty convinced it's not me :)