I've just tested this, and I believe it has to do with the way lwjgl handles key input, if you use the switcher and not the shortcut keys for it, it doesn't cause any problems, ctrl seems to get stuck, so hit ctrl again after switching if you use shortcut keys to make it resume playback.
Yup, that seems to do the trick! When I reported this previously the whole OS freezed because of this, but I believe that is an Ubuntu problem, not a problem with Spine. I'll just stick with pressing ctrl now and then
Something weird happened just now when I loaded a project; I suddenly had moved to a position at around 200000,-50000. Dunno what happened, but it took some scrolling to get back to 0,0. Maybe a button "zoom to center" might be handy?
Btw, do you have an ETA for Spine? Is it more likely to be January instead of April for instance?