Runme appears to look for full screen and/or topmost windows and hides itself if a full screen or topmost window is covering it. My guess is that the intention is to hide Runme if a game or something similar is open.
StrokeIt functions differently in the way it draws gestures on the screen. While it may not cause Runme to hide itself, the method Strokeit uses does allow for other issues such as:
While trying to work with Runme, it actually disappears on my system completely after 10 seconds (even when starting Runme without S+ or SI running). I thought it was due to multiple monitors, so I disabled my secondary monitor and Runme doesn't stay shown (I'm running Windows 8 64-bit). I have to kill the program via Task Manager and restart, which it doesn't stay visible very long. Again, this is without S+ or StrokeIt running at all.
In other words, this is really something for the Runme developer to address. While I understand that the issue is only when S+ is running with gestures drawn (for you), the problem is that Runme shouldn't consider the S+ draw window as a full screen application since it's transparent. The fact that it won't even stay visible on my screen, nor pop out when I move the mouse cursor to the edge of the screen, tells me the program could use some refinements to managing its state with a variety of configurations. Perhaps Runme could be enhanced to exclude certain windows, or not hide itself if a full screen window is transparent. In the end, I cannot control how Runme handles these situations; any change I made to S+ which might address Runme would introduce new problems for other people.
Activate window where gesture began:
Add this to your Global Lua:
function sp_before_action(gnm, gsx, gsy, gex, gey, gwd, gapp, gact)
--Activate the owning window where the gesture started
Unfortunately, I'm unable to reproduce this. Does it happen every time? Only when you drag and cancel a gesture? With or without the Keep Gesture Draw Window on Top preference checked? Could you perhaps make a quick video to demonstrate that issue?