Sorry to interrupt - not a good thing as it can disturb a train of thought...
But reading the entire thread, a few things I've noticed.
lunerceli - You're first screenshot shows 4 colums and 4 rows for desktops.
You haven't mentioned whether you have checked your Desktop size in 'CompizConfig Settings Manager'.
In CompizConfig Settings Manager, click on 'General Options' and then click on the 'Desktop Size' Tab.
To have the 'cube' working corectly, your Horizontal Virtual Size should be set at 4 and Vertical Virtual Size at 1.
Once done, reactivate Compiz and see if it makes a difference.
Sorry to interrupt Amir.