I am sure they will fix it eventually, and I know it seems like a relatively minor grip in a game as rich and engaging as this. Call it OCD RPG syndrome, or whatever. I just can't bring myself to play until this is fixed! I was amazed that there was no mention of this in their first major patch!
Every time I leave Sanctuary my happiness goes down and water and electric drop to 0. Beds also drop to an odd low number. I have manually assigned every single follower to their own bed, and verified that they go to the right one at night. Still, as soon as I leave, the resource tracking breaks and my happiness drops.
As soon as I fast travel or run back everything magically fixes.
This has been a widely reported issue. I will be patiently awaiting a fix but playing (and modding) other games until it is.
/signing off.