@RoverDude can I poke you about this? I'm having this issue as well with neither the "Start Habitat" or "Start Greenhouse" options effecting the craft animations. There are kerbals present on the ship, it has a connection, has power but it isn't working. If you pre-deploy in the VAB or SPH and launch it, the animation is running with it deployed and spinning but you again don't have any option to deflate the hab ring.
Here are some logs:
And some pictures if they help
Let me know if you need anything else This is KSP 1.3 by the way but I've noticed it happen on past versions.