I seem to remember having a similar problem with LunarCell early on, but haven't had that trouble lately. Are you using version 1.5? My problem is if I try to generate a texture larger than about 5000 px it will crash.
Oh, instead of uninstalling and reinstalling the whole filter, find the map it's using to generate the realistic clouds and delete it. I think that worked ... for some reason. Seems like a familiar solution anyway so it must have fixed something at one point.
For clouds try this, which you may already know about:
2922 different cloud maps a year
Might have to remove some coastline, but still handy.
Did the hacked version of LunarCell do anything special?
Speaking of pinching, FlamingPear (the LunarCell folks) distribute a batch of free filters that include filters like Make Cube Tile, Sphere Warp A, and Sphere Warp B which can be used on non-seamless textures to create proper maps for spheres.
Thanks for the insight into your textures, and the links, I'll definately have to incorporate those techniques.