Without any further details about your app, it's pretty difficult to diagnose any possible cause, I'd guess.
Also not exactly sure what you mean by "use mouse then leave it to disappear" .. I'm thinking that you mean "when you let the pointer sit idle for several seconds, and then it disappears"?
In LG webOS, there is a key event that is dispatched to the foreground app (assuming it's a HTML/Web App) when the pointer turns on and off. I'm not sure right off hand exactly what keyCode is sent along with it, but it's something that would never exist on a regular keyboard.
Perhaps you have some key handler that is being triggered, and interpreting it as something?