Note: I've seen this same behaviour with Hyperedit.
When starting in orbit and then staging, if the wrong portion of the ship gets 'controlled' and you use ] / [ to switch to the important portion, the camera will start to shake, as in the "Moving Over Terrain" situation. This will sometimes cause ships to disappear while doing EVA and other severe issues.
Note: I've seen this same behaviour with Hyperedit.
When starting in orbit and then staging, if the wrong portion of the ship gets 'controlled' and you use ] / [ to switch to the important portion, the camera will start to shake, as in the "Moving Over Terrain" situation. This will sometimes cause ships to disappear while doing EVA and other severe issues.