I had this problem too and then I was taught by Lax that I was misunderstanding the use of keymaps. I had two keymaps that I put on the same set of characters. Well IS then loads up both maps at the start and you are stuck with a jumbled mess.

So in closing only enable one keymap on your profile, have the other turn on with a toggle and your main needs a toggle as well. Also another thing I noticed was that if I do something funny while screens are loading they can get out of sync. Like clicking on a webpage so the main window minimizes, it doesnt happen often, but when it does it requires restarting all windows to fix.