I’m running 10.11.4 with six monitors (2 on a flashed Quadro 9800; 4 on an unflashed GTX 970) on a 4.1 Mac Pro flashed to 5.1 12 core 3.33 64Gb. I have 16 spaces (the maximum) for each monitor for a total of 96 spaces.
The behavior also happens with Yosemite.
With the exception of the Boot Screen monitor, I can’t get the application assignments to stay with each reboot. They switch from monitor to monitor. There’s a pattern to the change, but I haven’t figured it out completely.
I have the monitors set up as individual spaces and I use the Sync Grid option. The Applications stay assigned to the same grid, but shift from monitor to monitor upon reboot.
It doesn’t matter if I have Total Spaces auto launch or I manually launch it after the finder appears.
The Space numbers DO NOT change when I look at them with the Mission Control shortcut. Each monitor has the same Space Numbers assigned to them by Mission Control.
The Total Space Names for the monitors so not stay with the Space Numbers (I think that’s what is shifting everything)
I can use DisplaceSpaceManager to reassign the Total Space Names to the correct displays and spaces, but the Applications don’t follow the change - they stick to the random assignments Totals Spaces gives them when I launch Total Spaces.