Ok using the “New Loadout” option worked for me so far.
I deleted all of my current loadouts, then created new one. let the new one save then added a couple spells to my action bars and logged out. Much to my surprise when I logged back in was the spells where still there! 
This worked for me after a week of trying every suggestion out there, and hopes it helps others. Good luck all! 
I have it happening too but it seems to not be all characters it is on my lower characters
Save a loadout in the Talent menu. doesn’t matter what.
It appears to have the same issue macros sometimes have with syncing with the settings the server saves of our characters. Probably some kind of version mismatch so we have to let it do its thing fresh from scratch then restore our settings. Happens all the time on PTR/Beta.
Here’s how I restored my bar’s functionality:
Go to your “World of Warcraft_retail_\WTF” folder and back it up (Windows; select the WTF folder then right click>Select Send to>click Compressed (zipped) folder.
These are all of your settings; we will bring them all back later.
Now delete the WTF folder (but keep the backup you just made).
Log in to WoW on any character and enable all your bars. /reload at least twice to make sure it is indeed saving that all of your bars are enabled. Then fully log out of the game.
Now go back to your backed up WTF folder and restore it. In Windows select the WTF folder zipped folder then right click and select “Extract All…” Drag and drop the enclosed WTF folder back into the “World of Warcraft_retail_” folder and overwrite any files it asks you to.
Log back in and you should see that all bars are still enabled and all of your settings are also restored. Now you can enable/disable the bars as expected, without this whole rigmarole again.
Cheers!