It's almost certainly caused by a sound problem (at least in my experience).
Do you have any custom sound pack installed?
Also, does this happen to every single plane type, or only certain planes. If it only happens in a few planes, I'd delete the "Flaps" sound file for that/those particular plane(s).
I used to have this in my Spitfire XVI, which is why I remember it all.
<S>
Yossarian