ok it isn't PTA related because I reset my shaders to default and could still replicate the issue.  See my original post on the LM forums here. 

http://www.prepar3d.com/forum/viewtopic.php?f=6312&t=126196&p=164548#p164548

The workaround is to turn cloud casting off under the lighting section.  Obviously this means the sim doesn't look as good but its a workaround if it irritates you that much (like me). Brady  Software Engineer linked another thread with a chap reporting the same thing. He asked me to piggyback on his thread and copy my video into the post which I've done here.

http://www.prepar3d.com/forum/viewtopic.php?f=6314&t=125862

So hopefully it will get looked at.

It's quite funny they try to wipe the issue off in the sleeve of other addons, when it's a known and very obvious issue of how the core engine handles shadows and culling. 

30 minutes ago, Sethos1988 said:

It's quite funny they try to wipe the issue off in the sleeve of other addons, when it's a known and very obvious issue of how the core engine handles shadows and culling. 

Brady did nothing of the sort! He did suggest that "if the problem were caused by an addon..."

After which he admitted that this is a known issue:

Quote

We do have a known behavior bug with cloud casting turned on, which I thought only messed up shadows on the aircraft and not on the ground around it as well. Please refer to this post:

As a developer myself, I'm very much aware that every possibility must be explored and either confirmed as the proximate cause, or eliminated as a casual factor.

issue continues in V4.2   

Still the bug is here nearly a year later.

Potentially the engine should try to draw clouds within a given 'cone' between the user and the sun. That way it could still cull a unseen clouds but render the key ones that affect produce significant shadows locally. Wouldn't be perfect but its pretty awful at the moment so anything would be better.