First thing I would check is to see if my bed was still there and set as spawn point.
Someone/thing may have destroyed it and remade it.

Then I would suggest verifying local files. Library - right click on game name for properties - local files - verify.

If that won't work I would then suggest uninstalling the game <after backing up saves>
Manually navigate to the folder and delete it entirely.
Reinstall "clean" copy of game. <an uninstall may not remove everything, to make sure you have a good install you have to delete the file manually>

Add mods back in after you verify proper game function in a new game save.