I have seen the same problem and I have found a work around.
The trick is that you open up mission control and keep adding spaces through mission control. In my case I had two rows of 3 and wanted to add a 3rd row of 3. It didn’t work. I then thought remove one row and then add it again. Maybe the application is confused. Guess what after that I was limited to 3. Only after I increased by #screens to 9 in mission control I could configure TotalSpaces again.