Ironically, I, too, had a very similar issue regarding the cube cap (the minimize, maximize, close buttons are a completely different story and sound like an error with Emerald). I attempted changing the cube cap or the cube background to find that all the settings regarding the cube had somehow reverted to a time in which they were never set. Basically, everything regarding the cube reset and defaulted -- everything.
I never did find out the key combination to pull this back to complete order. Within the hotkeys area of the setup (where you're able to set the key combinations for certain actions) regarding the Desktop Cube or Rotate Cube, attempt to set the hotkey for rotating the desktop as being some random set of keys on your keyboard and it'll work accurately when pressing those keys upon saving. Sadly, I was forced to reinstall as I had no clue what went on and no clue how to set those settings to how they were manually. The new key combination I had personally set wasn't satisfactory for me.
I hope this helps, somewhat.