Thanks for the pointers Tony but I'm on top of most of that stuff
Hopefully the following may help anyone still struggling...
I'm not sure what was going on but I decided to do some tests enabling and disabling SMP and various options. I was more worried about the odd look of the "postage stamp" (dinner plate was the wrong expression as it's rectangular, not circular) effect of the overcast when viewed from above. FPS wasn't too bad for me.
For anyone struggling this is what I did just now which seems to have sorted multiple issues / niggles...
I rebooted gizmo which seemed to improve things a bit. This made me wonder if a full uninstall and re-install of SMP (*not* X-Plane) would help. When upgrading SMP I just used the installer to uninstall the old version so maybe this didn't fully clean everything. It's also entirely possible I used the same method upgrading from v2 --> v3 so there may be who knows what leftovers.
I uninstalled SMP and fired up X-Plane just to see what that did (baseline basically) and everything looked much better (wall to wall overcast which was what I was after with the weather I have set for testing) but withough the SMP finesse of course.
I then re-installed SMP. Haven't changed anything yet apart from disabling lens flare. (Geek aside - Note that I normally install from a NAS - I noticed when unistalling the NAS paths were being accessed. Before re-installing I copied the SMP installers to the same drive as X-Plane is installed. I'm running X-Plane SE.)
Results - fantastic. I now have realistic looking cloud cover at FL410 (not a tiny postage stamp immediately below me). FPS has shot up too. VRAM usage reported by MSI Afterburner has dropped by about 800K. Time to turn things up again
Conclusion: If you're having problems, reboot Gizmo uninstall SMP completely. Fire up XP and make sure things look how you expect. Note FPS. Install SMP. Check visuals. Note FPS. Smile hopefully. (X-Plane load times have dramatically reduced too).
Only one question / point - I have to assume rebooting Gizmo is *not* something that happens every time X-Plane is restarted! But that's for another day.
PS - just sat here in pause mode at FL410 over the Shetland Islands watching the sun come up and light the cloud tops. Stunning Time to go fly!