Yikes. No this is different. I can say this. I just recently played a mission on FATA and the transport chopper takes off and lands from the southern FOB fine from what I’ve seen. That said, I’ve seen this exact bug before too and boy is it terrible. Have you placed any objects near where the helipad/landing spot is? I was able to make it stop by deleting a lot of objects in the base in one of my missions (FWIW it was happening on Takistan to me).
If so, try deleting these objects. If not, and if you’re bored, does it happen if you play this?
http://steamcommunity.com/sharedfiles/filedetails/?id=960750742
I have noticed on FATA the southern FOB is making some choppers get halfway stuck in the ground, and they dance like crazy, but so far they seem to move and follow commands ok. I did have to delete one of th helipads though with the delete map object module just to make the weird bouncing stop. I doubt it’s related but if you want go ahead and try that mission out and see if the issue is still there for you. If the issue is gone in my mission, feel free to use it as a template for your own mission.
Are you using any AI mods at all? What mods are you using?