Yes, I am using FSX weather, and during the flights that have been giving me trouble I have been setting it at either "Thuderstorms," or "Building Storms." Does that make a difference?
Well, that is hard to tell. The rudder pedal movement that you see might just result from the fact that the autopilot is sophisticated enough to provide Auto Coordination (when rudder boost is off). So I think it would be very likely that what you're seeing is perfectly normal. The turbulence is rocking your wings, and the AP is simply Auto-coordinating with the rudder. So if the AP is on, and RB off, My guess is that what you are seeing is okay
, but if you want to pursue the matter:
1) See if this happens in calmer weather
2) Just as a troubleshooting method, consider this. The AP can only do Turn Coordination when the Rudder Boost is turned Off. (That is why the manual says you should turn it off when AP is In). So as a troubleshooting step, what happens if the AP is engaged and you leave RB on? Do you still get uncommanded rudder input?
3) There may be some of the famous 'S-turn' behavior, which is a real pain in the butt on certain other payware airplanes. You can look that up. The Stratocruiser isn't noted for falling victim to that, but I have seen a bit of it before. I use Active Sky & FSUIPC and there are definitely some settings you can use to eliminate it, but I'm not sure what steps you might take when using out-of-the-box FSX weather....FSX weather is kind of crappy and buggy to be quite frank. Are you using the wind smoothing options within FSUIPC?
As far as this happenning when the AP is NOT ON, that is a real head scratcher. You shouldn't be getting uncommanded rudder input when the AP is off, so that leads me to believe you could possibly have a problem with your controller. You've checked for duplicate axis mappings I assume? Assuming that your controllers are okay, The fishtailing you are reporting on landings is probably not a result of uncommanded rudder input. It could also have to do with assymetric thrust, poor FSX ground friction model that you are overcorrecting for, or just some gustiness in the wind. I don't know what your throttle setup is, but I've experienced a yaw motion before just because of stickiness in the Saitek throttles I use...you retard the throttles during the flare, but one of them sticks or spikes, and that will cause some yaw that takes you off the centerline.