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).