Do you have any soaring scenery? Try disabling it.
Are you using real-wolrd weather? It looks like a combination of cloud and ground fog. Very strange!
Emachines T3418 AMD 3400+ processor 2GHZ/256KB L2 Cashe 2Gig Ram 160Gig HDD NVidia GEForce 6100 GPU Running WinXP Home Can't believe it still works! Running FSX Standard with SP1 and SP2
Take everything I say with a grain of salt and maybe some pepper! There's no such thing as too much garlic!
Those arent the default clouds... wait, are you using the "simple clouds" option?
FWIW, it's a flight I do frequently, Kansai>Haneda, and this is the first time this oddity has occurred. Terrain is mesh and LC from Photo Japan Tokyo with GEPro filling in everywhere else, clouds are from REX, weather is ActiveSky, water is Zinertek. Other airports are SimmersSky with a few freeware sceneries. Using detailed clouds, 60%, with visibility controlled (not yet to my satisfaction) by FSUIPC.
It appears the transparent edge of the cloud image is being rendered and overriding any images behind it, but how or why that is happening is beyond me. This is not altitude dependent, that first screenshot was from 20k ft., these are much lower -
I have had similar problems recently with my clouds, sometimes there seems to be a ghost image of other clouds. I do not think using rex as an alternative is the solution, why should you have to pay for something when previously you have managed without it?
Disable all your sceneries. If the problem persists, check your Display/Weather settings.