When I press ok in preferences and then immediately press and hold ctrl (ignore key), then the key "gets stuck". it is not released on actual release. No gestures work then. The same happens if you ok the preferences and then use a gesture that 'presses ctrl'. Funny that the option to 'disable strokesPlus' is not on while the strokes don't work at all.
Ctrl is then released only on another press and release of the ctrl when you switch to another app.
BUT in all this one thing is necessary to make this bug happen: that the S+ app is "focused" when you first press Ctrl. Hard to describe but in XP you can see that the focus is not on any other window but on S+ app in systray.
This has confused me several times, it might also be an issue with other earlier versions of S+.
Ah, ok. "Complicated internal reason" can be quickly solved by S+ program sending alt+tab to system after preferences are okayed (when the S+ window has focus). Focus then immediately gets to another app, possibly the one on top of stack.
Perhaps this would be the best workaround until you actually do a full solution.