I noticed this same issue today, and tested it for a while. From the Googling I did, it looks like a similar issue reported back in time, I think it was 2011.
If you set weather to standard, and set cloud density below 9 (for sure I checked 1,6,7,8. Load into the cockpit of your AC, you will see the clouds (looks great too). Then F11, or F2 around the map for a few times looking at the clouds in the area of view. Then go back to your AC (F1), and the clouds will be gone.