I've just uploaded an update for the HM3 alpha that hopefully will fix the problem with the layers getting hosed up beyond all belief when you load saved character. Unfortunately it looks like this has also broken the "Move to bottom" function and introduced a new error when loading a saved character where things are getting masked to the wrong items.
But, I wanted to put this up there for now to see if at least the layering problem is fixed. Give it a shot and let me know -- I THINK you can load old characters and it ought to work properly.
