TotalSpaces2 desktop confusion with external display

Running TS2 on a Macbook Pro with an external display attached and 10.11. With external display connected, I have defined a 3x3 grid of desktops. This all works fine.

The problem occurs as soon as I disconnect the external display, at which point I suddenly end up with this:

If I open new windows in this environment (without external display attached), the windows appear to be moved to random other spaces when the external display is reconnected. I haven’t noticed a pattern here, just that it appears unpredictable.

I never had this problem with TS1 and OSX 10.8, so I assume this is either a bug or that I have some bad setting somewhere…?

For reference - one solution is to turn off Displays have separate spaces mode in Mission Control preferences.

Yes, this appears to have fixed the problem. Thank you!!!