Same issue here. Whenever I leave Sanctuary, my beds go to 1, and my power and water go to 0.
I read somewhere else that if you open the workshop UI while in Sanctuary, and then walk out of town until it auto closes the workshop UI, you should be able to fast travel without this happening. It doesn't seem to work all the time, but it does seem cause the bug to happen less often.
This bug is really annoying, though.. I put a lot of work into Sanctuary, and now I pretty much have to keep the workshop tab in the pip-boy open all the time so I can monitor the resources there and travel back when they start bugging out.
:EDIT I completely redid the bed situation in my Sanctuary Hills, and I think I've finally avoid beds and power disappearing when leaving Sanctuary Hills.
If you place your beds and generators on wood floors, they will stay loaded when you fast travel away. It seems like if you place them on any player placed structure they will remain loaded. I'm still having a problem with my water resource going to 0, though, because they have to be on dirt or in the water.