Desktop Photos Disappearing

I just updated to OS 10.12.4 using the combo (which was recommended by Cocktail). Since then, whenever I shut down and restart, most (but not all) of the photos for each desktop vanish. Mostly, they are photos I’ve selected from my Photos library and it happens whether I do it from System Preferences or directly from Photos.
I was using Total Spaces 2.5 and I saw there is a 2.5.1 which I’m now trying.
Am I doing something wrong?

I have no good idea why this would be. Sometimes I have had to re-select desktop pictures, but usually they continue to work after that. I will try selecting from photos library to see if there some issue there.

Note that TotalSpaces is built on top of macOS mission control desktops, and macOS itself maintains the database of desktop backgrounds. TotalSpaces reads the information when it needs to display the overview grid, but otherwise doesn’t change anything there. That’s why I don’t have much knowledge about what might be happening, as it’s likely on Apple’s side.

BTW, version 2.5.4 is the latest version of TotalSpaces2

Hi Stephen and thanks for responding.
So I installed the latest version, did the thing in Terminal, and tried placing photos on my various screens again. It seems that if I log off and on, they remain, but if I shut down then they disappear. Except for one screen which stays solid blue and two others that retain the same photo which I put on long ago. I’ve tried exporting the photos from Photo to the pictures folder where that one photo that stays is kept, but that also doesn’t work. If I weren’t stuck with the default photo of the mountains, maybe I wouldn’t care.
I’m going to try installing some of Apple’s photos and see if they remain.

I think I figured it out. I’m using a second screen and that was identified as the primary. So I switched primary back to the MacBook Pro screen, reset all the photos, and then switched it back. I shut down and restarted (twice) and all the photos returned to correct Total Spaces screens as before. I also made sure that System Preferences was set to “all screens” as an Apple article said to do.
Hope this helps someone else sometime.

Ah, great you figured it out!