In the TE, when I had two spawn points very close to each other and both selected, spawns 1 and 5, the TE's GUI reported that spawn pt 1 was rotating when I had 5 highlighted. Five refused to rotate until I deselected 1. Moving either spawn worked, as did the U,R,L,D buttons.
It these TE sessions, I would typically set circles to 3, icons on, numbers on, and show entry points. At some point, the circles will become garbled. This happens in the AH2 TE as well. It's more likely after a save but can happen at any time. The entry points get the GMS's 3 mile circles and in the Beta. In the situation above with pts 1 and 5, spawn pt. one completely disappeared.
EDIT: Left over from the AH2 TE, when setting objects for any zone but zone one, it's necessary to change the zone number repeatedly. I usually fix it in the oba file but that wouldn't be necessary if the zone number stayed put once you set it for zone 2 or 3.