Hmm... I wouldn't even know where to start, even had to google to find out what ion3 is
From your description, I would guess it is something in wxAUI that goes wrong. That stuff is not managed by ourselves. I'm surprised it should work in the nghtly builds, though... don't think there were any changes related to layout/windowing at all for months.
Could you try running the wxAUI demo (in the wxWidgets "samples" directory) to see if it goes wrong in that one too?
Maybe it's something with the "transparent overlay hint" or such (there are tweakables in the demo to turn on/off all kinds of features). If that is really it and you find out what it needs to work, it should be easy to fix.
Otherwise, I see very little hope.