I have the same problem. I found that by lowering the cloud coverage area and applying the change eliminates the stutters. The good news is... I can then go back and increase the cloud coverage area to what it was before I lowered it with no stutters being reintroduced.
I never experienced these stutters in SkyMaxx 3.1, only in 3.2 since it was installed a couple of days ago. And the stutters usually begin to appear when I start my pushback OR very shortly after takeoff. To generalize more about "when" this occurs... it's early in the trip and shortly after my aircraft has begun to "move", presumably requiring the system to draw clouds more dynamically relative to the aircraft's changing position. Happily, they NEVER come back at any point in throughout the rest of my journey once I've eliminated them.
For me, it's manageable, but unacceptable to have to do that.
That said, the improved performance of the clouds is very noticeable and much appreciated. It's allowed me to really increase the coverage area substantially and I now get a better depth of cloud cover.