For whatever reason the command pods from Near Future Spacecraft are bugging out for me. When I put one in for a craft, it places fine. But if I then click it to move it anywhere it disappears (along with anything attached to it / it's attached to). It also doesn't allow the craft to be saved. I'm running 1.8.1 with the mod installed via CKAN.
I'm running it with a lot of other mods, though it'd be a bit tedious to list them all out. Guess I'll just see if this is a known issue with a specific mod / kind of mod first. If that doesn't help then I'll list out all the mods.