@Shagga I have observed the problem you describe with Air Staging Beacons (Seraphim) and I've seen it with Aeon as well (and it probably happens with the other factions too). Until tonight I just thought they were broken and in a way (UI/UX) they are. In order to "deploy", you have to "sub-select" the individual air units at the menu presented for the repair/refuel building and then deploy. If there is a fast way to select all of the parked units at the building's menu, I haven't found it yet, I've only been able to select individually (ugh). Curiously, even "select all air units (CTRL+A)" does not select air units parked on the r/r building (which seems really broken). I would think the way it would work is that parked units deploy when the deploy order is given to the r/r building. And maybe it's preference, but when I tell air units to go home and repair/refuel, they should do their business and then get off the r/r building so another air unit can use it. It appears that telling air units to return home to repair/refuel is what causes them to park on the air staging building (and get "stuck").
I'm just getting into FAF but the behavior might make sense for something like a "hangar" and maybe there is a mod for that -- if not might be a great addition. "AHA! Feel the power of the air force you didn't think I had. Muahahaha!"
"Dock" is the name of the command to send air units to nearest air staging facility. After more testing (playing) it looks like air units just get "stuck" (require manual deploy) sometimes. Not power locked, not told to return to air staging facility. At least I know how to get them back in the game now. Previously I was CTRL+K'ing the air staging facilties - LOL!