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I think I had the same problem, just ran into it today.
I have a 2x2 grid (4 screens) on 1 monitor. Randomly, not sure what causes it, two of the screens will swap spaces. So instead of Top:1,2 Bottom:3,4, it'll be Top:3,2 Bottom 1,4 (1 and 3 swapped spaces.)
It must be tied to Octopus. I use Octopus for KVM, and KeyClone for broadcasting on 1 machine. I run my main on one computer, and my 4 followers with keyclone on the second. If I click a window on the second, then move the mouse to my main, the focused window gets swapped into position 1 (top-left). If I focus on a new window and move the mouse, that one gets swapped.
It also only happens when using maximizer through KeyClone. If I manually set up maximizer and launch the clients that way it doesn't happen.
I will be in the irc room from 3:00 pm CST to 10:00 pm CST most days. I can be found there.
I deleted (after a LOT of work) ICQ because it really..... yea. lets just say a lot of expletives later.