Greetings all. This problem persists even on real Macs. The root of the problem and the fix is easy. It seems if you are using PCI GFX as your main display in conjunction with internal graphics, you will get a new desktop space for EVERY monitor you have plugged in after a restart. Meaning if you have 3 displays, 2 extra will appear every restart. To solve this simply move the MenuBar in Monitor Arrangement to IGPU and no more multiple Desktop spaces. The downside is you have your IGPU as your main and not your significantly more powerful PCI GFX.