Spaces get messed up (mixed or not changed)


I am using Total Spaces 2 now for a few weeks to get back to the workflow I used to in Snow Leopard (which I cannot use anymore with a new MacBook).
Currently I run into a weird behaviour:
I created 6 Spaces and named them differently in a 2x3 grid. Further I connected an external display and used the setting of mission control, so the external desktop is the same space as the local one (so I dont get 12 spaces when disconnecting).

But: When I switch the spaces through mission control everything works as expected (but I don’t like the arrangement in one long horizontal line). If I use Total Spaces in most cases the application windows are mixed up, f.e. if I have Excel on Space 1 and Finder on Space 2 the result after switching spaces is that I can see both Applications at the same time on the same space – while they are definitely still on different spaces in Overview Grid or Mission Control.

Is there any setting which I messed up or has someone else the same behaviour? I am using El Capitan with SIP (enabled with debugging like the blog entry) on a MacBook Pro 15 (2015).


Is nobody out there with the same problem/behaviour?

I am having this problem also. It is not completely predictable.
But when it happens, switching to Mission Control is my workaround.
This just started with my last update to 2.4.6.

Finally thinking I found the problem:
MenuEverywhere activated: Spaces messed up
MenuEverywhere deactivated: Everything works fine

Any workarounds?
I like to have multiple menu bars, but not that many spaces if I disconnect my notebook from the docking station. Therefore I cannot use the “each monitor has different spaces” switch :frowning: