SkyMaxx Pro does nothing that would affect winds or your weather radar display. That all comes from X-Plane's internal weather system. Even with RWC, we don't actually "inject weather," we just read the weather data that's provided to us from X-Plane. RWC's job is to interpret that in more detail to produce localized areas of clouds in SkyMaxx Pro.
That all said - if you're seeing nothing but clear skies regardless of what the default X-Plane weather and your radar is saying, I suspect this may be a licensing issue. If SkyMaxx Pro cannot validate its license, it will refuse to draw its clouds, leading to clear skies no matter what. There should be a message to this effect in your log.txt file; if you could post that we could look for it.
Another possibility is that it's a timing issue and the new weather conditions appeared in X-Plane after SkyMaxx Pro already set up the clouds for the scene. In this case, the new weather should appear within a few minutes, but you can force it to happen immediately with the "force weather reload" option in the SkyMaxx Pro menu.