I purchased the raised key model for better typing control, and at least half the times I try to use it, the Surface doesn't recognize that its there. Have to pull it off and on a few times to get it to actuate.
I have the touch model and I have sort of have the same issue. When I have the cover folded all the way so I can use it as a tablet, I use the screen KB of course. Then when I fold it to use the touch keyboard and takes a while for the keyboard to be active. Usually I have the settings to switch over. If thats the same issue as you, then yeah, it's annoying, but hope it gets fixed.