Nothing changed in 4.6 with regards to cloud formations, unless it's a storm system. I suspect you're flying around a corner of one of X-Plane's one-degree tile boundaries. When you cross one of the boundaries, X-Plane changes its internal coordinate system and we need to re-generate the clouds that surround you.
Also, make sure "never change visible weather" is activated in RWC if you're using it and flying with real world weather. Otherwise, the culprit may be some third-party weather injector you're using that's updating the weather too frequently.
SMP provides a variety of sky color sets if the one you're using isn't to your liking. Our Hosek-Wilkie model is the most accurate, but we're forced to blend it with X-Plane's own sky near the horizon in order to smoothly blend into X-Plane's haze and fog effects. I would imagine this could lead to some inconsistencies in some situations. If that's a deal-breaker for you, try one of the other sky color sets or the default setting.