The start menu overlapping the taskbar when the taskbar is on the left or right hand side of the screen is perfectly normal and expected. This is exactly the same as on Windows 7.
The issue with it being under when you have autohide on isn't something I could reproduce, but I will see if we can add additional code to force it to be above just in case.
Regarding the feature to go direct to the desktop, this hasn't been directly impacted by any windows updates, but it may be they have slowed your machine startup a little. This is especially true of reboots after installation of system updates as the machine will take a very long time to login and Start8 isn't expecting this.
The 1.01 update thats in development should make this a little more forgiving of delays.