I know what you mean. I saw it happen only once to me in the 757 and that was when I was using real weather, but that was in P3D*, never FSX, but it turned out that when I did this: Options > Settings > Display > Weather and checkmark (tick) the Disable turbulence and thermal effects on aircraft, it would uncheck it (remove the tick) as soon as I exited the settings and returned to P3D. I was able to stop it from preventing me from making the changes, so I no longer have the problem.

* Captain Sim don't support P3D. Only FSX.