Error 2 occurs when the characters received during the update aren't recognized. This means something is coming through but at the wrong baud rate possibly. If you are using the SD Update software, it sets the baud rate for you so I'm not sure what your problem might be. The update version doesn't matter.
The other problem sounds like mixed up scene data. If you are building new scenes from old, you will have problems if the old scenes used a different setup than what's current. The best solution is to clear the scene buffer before starting a series of new scenes. Hold the black switch for 1 sec. and then start building new scenes from a blank slate. Use these new scenes as the starting point.