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